Compositions, methods, modules and instruments for automated nucleic acid-guided nuclease editing in mammalian cells

ABSTRACT

This invention relates to compositions of matter, methods, modules and instruments for automated mammalian cell growth, reagent bundle creation and mammalian cell transfection followed by nucleic acid-guided nuclease editing in live mammalian cells.

RELATED CASES

This application claims priority to U.S. Ser. No. 63/092,499 filed 15 Oct. 2020, entitled “Compositions, Methods, Modules and Instruments for Automated Nucleic Acid-Guided Nuclease Editing in Mammalian Cells” and U.S. Ser. No. 63/014,944, filed 24 Apr. 2020, also entitled “Compositions, Methods, Modules and Instruments for Automated Nucleic Acid-Guided Nuclease Editing in Mammalian Cells.”

FIELD OF THE INVENTION

This invention relates to compositions of matter, methods, modules and instruments for automated mammalian cell growth, reagent bundle creation and mammalian cell transfection followed by nucleic acid-guided nuclease editing in live mammalian cells.

BACKGROUND OF THE INVENTION

In the following discussion certain articles and methods will be described for background and introductory purposes. Nothing contained herein is to be construed as an “admission” of prior art. Applicant expressly reserves the right to demonstrate, where appropriate, that the methods referenced herein do not constitute prior art under the applicable statutory provisions.

The ability to make precise, targeted changes to the genome of living cells has been a long-standing goal in biomedical research and development. Recently various nucleases have been identified that allow manipulation of gene sequence; hence, gene function. The nucleases include nucleic acid-guided nucleases, which enable researchers to generate permanent edits in live cells. Editing efficiencies frequently correlate with the concentration of guide RNAs (gRNAs) and repair templates (e.g., donor DNAs homology arms) in the cell, particularly in mammalian cells. That is, the higher the concentration of gRNA and repair templates, the better the editing efficiency. Further, it is desirable to be able to perform many different edits in a population of mammalian cells simultaneously and to do so in an automated fashion, minimizing manual or hands-on cell manipulation.

There is thus a need in the art of nucleic acid-guided nuclease gene editing for improved compositions, methods, modules and instrumentation for increasing nucleic acid-guided nuclease editing efficiency and throughput in live mammalian cells. The present invention satisfies this need.

SUMMARY OF THE INVENTION

This Summary is provided to introduce a selection of concepts in a simplified form that are further described below in the Detailed Description. This Summary is not intended to identify key or essential features of the claimed subject matter, nor is it intended to be used to limit the scope of the claimed subject matter. Other features, details, utilities, and advantages of the claimed subject matter will be apparent from the following written Detailed Description including those aspects illustrated in the accompanying drawings and defined in the appended claims.

The present disclosure relates to compositions, methods, modules and automated instrumentation for making edits in a mammalian genome. Efficient editing requires many excess copies of editing cassettes—comprising a gRNA and a repair template (e.g., donor DNA)—in the cell nucleus. In order to perform highly-multiplexed editing in a single reaction, it is necessary to co-localize the cells with many clonal copies of each editing cassette. Thus, the present compositions and methods entail making “reagent bundles” comprising many (hundreds of thousands to millions) clonal copies of an editing cassette and delivering or co-localizing the reagent bundles with live mammalian cells such that the editing cassettes edit the cells and the edited cells continue to grow.

The automated instruments envisioned herein include a module in which to grow the mammalian cells to be transfected, a module in which to transfect and edit the cells, and a module in which to pool and from which to collect the cells after editing. Herein are described three alternative modules—a rotating growth module, a tangential flow filtration module, and a bioreactor—for growing the cells both on-instrument as one module of the automated instrument or off-instrument prior to the start of the automated process. Transfection and editing take place in a microfluidic device or “chip” which are available commercially through, e.g., microfluidic ChipShop™ GmbH (Jena, Germany); uFluidix™ (Toronto, Canada); Microflexis™ (Hamburg, Germany); and microLIQUID™ (Gipuzkoa, Spain). Alternatively, once the cells and reagents are encapsulated in droplets/emulsion, the droplets/emulsion may be transferred or ported to the bioreactor for incubation and editing, as well as subsequent emulsion breaking. Moreover, the bioreactor may be used to generate the emulsion using the impeller.

Thus, in some aspects there is provided a method for transfecting and performing nucleic acid-guided nuclease editing in mammalian cells in an automated editing instrument comprising the steps of: providing an automated closed cell editing instrument comprising a growth module and a microfluidic module; growing mammalian cells in the growth module; synthesizing a library of editing cassettes off-instrument, wherein each editing cassette comprises a different gRNA and donor DNA pair; generating, in the microfluidic module, a first plurality of aqueous droplets in a first immiscible carrier fluid, wherein the first plurality of aqueous droplets comprise dNTPs, primers, polymerase and an editing cassette, and wherein each aqueous droplet of the first plurality of aqueous droplets on average comprises one or no editing cassette; providing, in the microfluidic module, conditions to allow amplification of the editing cassettes in the first plurality of aqueous droplets; separating aqueous droplets with amplified editing cassettes from aqueous droplets without amplified editing cassettes; generating, in the microfluidic module, a second plurality of aqueous droplets in a second immiscible carrier fluid, wherein the second plurality of aqueous droplets comprises transfection reagents and a nucleic acid-guided nuclease or nuclease fusion or a coding sequence for a nucleic acid-guided nuclease or nuclease fusion; adding, in the microfluidic module, the first plurality of aqueous droplets with the amplified editing cassettes to the second immiscible carrier fluid comprising the second plurality of aqueous droplets; merging, in the microfluidic module, on average one of the first plurality of aqueous droplets with the amplified editing cassette with on average one of the second plurality of aqueous droplets comprising transfection reagents resulting in aqueous droplet reagent bundles; generating, in the microfluidic module, a third plurality of aqueous droplets in a third immiscible carrier fluid, wherein the third plurality of aqueous droplets comprises the mammalian cells grown in the growth module; adding, in the microfluidic module, the aqueous droplet reagent bundles to the third immiscible carrier fluid comprising the third plurality of aqueous droplets comprising the mammalian cells; merging, in the microfluidic module, on average one aqueous droplet reagent bundle with on average one aqueous droplet comprising the mammalian cells to produce merged droplets; providing, in the microfluidic module, conditions for cell transfection and editing; transferring the merged droplets to the growth module; and demulsifying the merged droplets in the growth module resulting in pooled merged droplets.

In some aspects of this method, the merging step is accomplished by a localized electric field, providing locally a chemical that disrupts or destabilizes the surfactant in the second and/or third immiscible carrier fluids, or use of a textured surface in a flow path of a microfluidic channel through which the second and/or third immiscible carrier fluids flow. In some embodiments, the first, second and third immiscible carrier fluids are the same immiscible carrier fluid, and in some aspects, the first, second and third immiscible carrier fluids are a different immiscible carrier fluid.

Also provided herein is a method of transfecting and performing nucleic acid-guided nuclease editing in mammalian cells in an automated editing instrument comprising the steps of: providing an automated closed cell editing instrument comprising a growth module, a microfluidic module and a solid wall module; growing mammalian cells in the growth module; synthesizing a library of editing cassettes off-instrument, wherein each editing cassette comprises a different gRNA and donor DNA pair; generating, in the microfluidic module, a first plurality of aqueous droplets in a first immiscible carrier fluid, wherein the first plurality of aqueous droplets comprise dNTPs, primers, polymerase, a nucleic acid-guided nuclease or nuclease fusion or a coding sequence for a nucleic acid-guided nuclease or nuclease fusion and an editing cassette, wherein each aqueous droplet of the first plurality of aqueous droplets on average comprises one or no editing cassette; polymerizing, in the microfluidic module, the first plurality of aqueous droplets resulting in reagent bundle gel beads; providing, in the microfluidic module, conditions to allow amplification of the editing cassettes in the reagent bundle gel beads; separating reagent bundle gel beads with amplified editing cassettes from reagent bundle gel beads without amplified editing cassettes; delivering the reagent bundle gel beads comprising amplified editing cassettes to a solid wall module comprising wells, wherein the wells comprise the mammalian cells and are sized so as to be able to accommodate only one reagent bundle gel bead; dissolving, in the solid wall module, the reagent bundle gel beads comprising amplified editing cassettes in the wells; providing transfection reagents to the wells in the solid wall module; providing conditions to allow transfection and editing in the mammalian cells in the solid wall module; growing the mammalian cells in the solid wall module; dislodging the mammalian cells from the wells in the solid wall module; and pooling the cells.

In some aspects of this embodiment, the solid wall module is a solid wall isolation, incubation, and normalization (SWIIN) module, and in some aspects, the SWIIN module comprises at least 200,000 microwells with a volume of approximately 2.5 nl. In some aspects, the SWIIN module comprises a heater and a heated cover.

Also in some aspects of this embodiment, the reagent bundle gel beads comprise polyacrylamide with disulfide crosslinkers, and in some aspects, the reagent bundle gel beads are dissolved by exposure of the reagent bundle gel beads to a reducing agent such as β-mercaptoethanol, dithiothreitol (DTT), (2S)-2-amino-1,4-dimercaptobutane (dithiobutylamine or DTBA), or tris(2-carboxyethyl) phosphine (TCEP). In some embodiments, the first, second and third immiscible carrier fluids are the same immiscible carrier fluid, and in some aspects, the first, second and third immiscible carrier fluids are a different immiscible carrier fluid.

In yet another embodiment, there is provided a method of transfecting and performing nucleic acid-guided nuclease editing in mammalian cells in an automated editing instrument comprising the steps of: providing an automated closed cell editing instrument comprising a growth module, a microfluidic module and a solid wall module; growing mammalian cells in the growth module; synthesizing a library of editing cassettes off-instrument, wherein each editing cassette comprises a different gRNA and donor DNA pair; generating, in the microfluidic module, a first plurality of aqueous droplets in a first immiscible carrier fluid, wherein the first plurality of aqueous droplets comprise dNTPs, primers, polymerase, a nucleic acid-guided nuclease or nuclease fusion or a coding sequence for a nucleic acid-guided nuclease or nuclease fusion and an editing vector, wherein each aqueous droplet in the first plurality of aqueous droplets on average comprises one or no editing vector and wherein each aqueous droplet also comprises a transformation agent; polymerizing, in the microfluidic module, the first plurality of aqueous droplets resulting in reagent bundle gel beads, wherein the reagent bundle gel beads are degradable; providing, in the microfluidic module, conditions to allow amplification of the editing cassettes in the reagent bundle gel beads; functionalizing a surface of the polymerized reagent bundle gel beads, wherein the functionalizing allows for capture of mammalian cells on the surface of the polymerized reagent bundle gel beads; depositing the mammalian cells grown in the growth module on the surface of the polymerized reagent bundle gel beads; co-localizing, in an editing module, non-degradable microcarriers with a functionalized surface with the functionalized polymerized reagent bundle gel beads, wherein the functionalized surface on the non-degradable micorcarriers allows for capture of mammalian cells on the surface of the non-degradable microcarriers; degrading, in an editing module, the polymerized reagent bundle gel beads to release the editing vectors and to release the mammalian cells from the surface of the polymerized reagent bundle gel beads; and capturing the mammalian cells on the surface of the non-degradable microcarriers.

In aspects of all these embodiments, the growth module may be a rotating growth module, a tangential flow filtration module or a bioreactor module. In some aspects of these embodiments, the mammalian cells are grown on microcarriers.

In some aspects of these embodiments, the step of sorting cells, droplets or gel beads is accomplished by electrophoresis; dielectricphoresis; acoutstrophoresis; optical sorting; or magnetophoresis.

These aspects and other features and advantages of the invention are described below in more detail.

BRIEF DESCRIPTION OF THE DRAWINGS

The foregoing and other features and advantages of the present invention will be more fully understood from the following detailed description of illustrative embodiments taken in conjunction with the accompanying drawings in which:

FIG. 1A depicts an exemplary workflow employing liquid-partitioned (e.g., droplet) delivery for editing mammalian cells grown in suspension. FIG. 1B depicts one embodiment of a droplet generator used in this FIG. 1B to partition editing cassettes in a Poisson distribution. FIG. 1C depicts an exemplary method for generating partitioned clonal copies of editing cassettes and transfecting and editing live mammalian cells in the droplet partitions.

FIG. 2A depicts an exemplary workflow employing solid wall partitioning and editing of mammalian cells grown in suspension. FIG. 2B depicts an exemplary method for encapsulating clonal copies of editing cassettes in gel beads. FIG. 2C depicts an embodiment of a method for preparing gel bead reagent bundles for transfecting cells in a solid wall partitioning module. FIG. 2D depicts transfecting and editing live mammalian cells in a solid wall partitioning module.

FIG. 3A depicts one embodiment of a growth module, consisting of a rotating growth vial for use with the cell growth module described herein and in relation to FIGS. 3C-3E. FIG. 3B illustrates a top-down view of the rotating growth vial depicted in FIG. 3A, showing optional internal “fins” or “paddles” for growing mammalian cells. FIG. 3C is a perspective view of one embodiment of a rotating growth vial in a cell growth module housing. FIG. 3D depicts a cut-away view of the cell growth module from FIG. 3C. FIG. 3E illustrates the cell growth module of FIG. 3C coupled to LED, detector, and temperature regulating components.

FIG. 4A depicts retentate (top) and permeate (middle) members for use in a tangential flow filtration module (e.g., cell growth and/or concentration module), as well as the retentate and permeate members assembled into a tangential flow assembly (bottom). FIG. 4B depicts two side perspective views of a reservoir assembly of a tangential flow filtration module. FIGS. 4C-4E depict an exemplary top, with fluidic and pneumatic ports and gasket suitable for the reservoir assemblies shown in FIG. 4B. FIGS. 4F and 4G depict a retentate reservoir assembly comprising one or more strainers or sieves which may be used to dissociate cells in the tangential flow filtration module.

FIGS. 5A-5G depict various components of an embodiment of a bioreactor useful for growing and transducing mammalian cells by the methods described herein. FIG. 5H-1 and FIG. 5H-2 depicts an exemplary fluidic diagram for the bioreactor described in relation to FIGS. 5A-5G. FIG. 5I depicts an exemplary control system block diagram for the bioreactor described in relation to FIGS. 5A-5G.

FIGS. 6A-6C depict an embodiment of a solid wall isolation incubation and normalization (SWIIN) module. FIG. 6D depicts the embodiment of the SWIIN module in FIGS. 6A-6C further comprising a heater and a heated cover.

FIG. 7A is a representation of a photomicrograph of aqueous droplets comprising a lipoplex assembly in an immiscible carrier fluid and a representation of a photomicrograph of the demulsified lipoplex assembly being combined with mammalian cells in aqueous droplets in an immiscible carrier fluid. FIG. 7B is a bar graph of the efficiency of HEK293T cells transfected in bulk and HEK293T cells transfected in droplets where the droplets are not washed or are washed post-transfection.

FIG. 8A depicts a method for determining purity of cells after transfection and demulsification. FIG. 8B is a bar graph showing the retained purity of cells transfected, edited and demulsified by the methods described herein.

FIG. 9A is a graph plotting the copy number of differently-sized amplified nucleic acids (e.g., 500 bp, 2000 bp and 10,000 bp) per droplet in differently-sized droplets. FIG. 9B is a graph plotting the cell coverage for 500 bp amplicons for droplets of differing size.

FIG. 10 depicts an engine plasmid and a library of amplified editing cassettes.

FIG. 11 depicts a map for an editing cassette.

FIGS. 12A and 12B are graphs demonstrating that the materials comprising the components of the bioreactor are biocompatible.

FIG. 13 comprises three graphs demonstrating that iPSC culture and cell expansion in the bioreactor described herein is comparable to cell culture and expansion in a CORNING® spinner flask and in a traditional cell culture plate.

FIG. 14 is a graph showing that media exchange at ˜200 ml/minute does not impact cell growth.

FIG. 15 is a series of four graphs demonstrating that up to five rounds of impeller shear is tolerated by iPSCs with no negative effects on re-seeding.

FIG. 16 shows a workflow at upper right, a table reporting percent efficiency at various steps in the workflow at lower right, and a graph showing the replicates measuring the percent efficiency at various steps in the workflow at left.

FIG. 17 is a graph showing that cell seeding and expansion are both unaffected by the impeller-shear based passaging protocol.

FIG. 18 at top are histograms showing the fluorescent expression distribution measured via flow cytometry of the cell population for individual stemness marker expression. FIG. 18 at bottom left is a bar graph showing a stemness panel (FACS % positive) for cells in the bioreactor described herein, on laminin plates and on MATRIGEL® plates (CORNING® BIOCOAT™ MATRIGEL® 6-well plates (Corning, Inc., Glendale, Ariz.)). FIG. 18 at bottom right is a bar graph showing a stemness panel (FACS median fluorescence) for cells in the bioreactor described herein, on laminin plates and on MATRIGEL® plates (CORNING® BIOCOAT™ MATRIGEL® 6-well plates (Corning, Inc., Glendale, Ariz.)).

FIG. 19A-19F show a series of panels, both % positive and median fluorescence, demonstrating that iPSCs grown in the bioreactor described herein maintain differentiation potential comparable to iPSCs cultured on laminin plates and in MATRIGEL® plates (CORNING® BIOCOAT™ MATRIGEL® 6-well plates (Corning, Inc., Glendale, Ariz.)).

It should be understood that the drawings are not necessarily to scale, and that like reference numbers refer to like features.

DETAILED DESCRIPTION

All of the functionalities described in connection with one embodiment are intended to be applicable to the additional embodiments described herein except where expressly stated or where the feature or function is incompatible with the additional embodiments. For example, where a given feature or function is expressly described in connection with one embodiment but not expressly mentioned in connection with an alternative embodiment, it should be understood that the feature or function may be deployed, utilized, or implemented in connection with the alternative embodiment unless the feature or function is incompatible with the alternative embodiment.

The practice of the techniques described herein may employ, unless otherwise indicated, conventional techniques and descriptions of organic chemistry, polymer technology, molecular biology (including recombinant techniques), cell biology, biochemistry and sequencing technology, which are within the skill of those who practice in the art. Such conventional techniques include polymer array synthesis, hybridization and ligation of polynucleotides, and detection of hybridization using a label. Specific illustrations of suitable techniques can be had by reference to the examples herein. However, other equivalent conventional procedures can, of course, also be used. Such conventional techniques and descriptions can be found in standard laboratory manuals such as Green, et al., Eds. (1999), Genome Analysis: A Laboratory Manual Series (Vols. I-IV); Weiner, Gabriel, Stephens, Eds. (2007), Genetic Variation: A Laboratory Manual; Dieffenbach, Dveksler, Eds. (2003), PCR Primer: A Laboratory Manual; Mount (2004), Bioinformatics: Sequence and Genome Analysis; Sambrook and Russell (2006), Condensed Protocols from Molecular Cloning: A Laboratory Manual; and Sambrook and Russell (2002), Molecular Cloning: A Laboratory Manual (all from Cold Spring Harbor Laboratory Press); Stryer, L. (1995) Biochemistry (4th Ed.) W.H. Freeman, New York N.Y.; Gait, “Oligonucleotide Synthesis: A Practical Approach” 1984, IRL Press, London; Nelson and Cox (2000), Lehninger, Principles of Biochemistry 3^(rd) Ed., W. H. Freeman Pub., New York, N.Y.; Viral Vectors (Kaplift & Loewy, eds., Academic Press 1995); all of which are herein incorporated in their entirety by reference for all purposes. For mammalian/stem cell culture and methods see, e.g., Basic Cell Culture Protocols, Fourth Ed. (Helgason & Miller, eds., Humana Press 2005); Culture of Animal Cells, Seventh Ed. (Freshney, ed., Humana Press 2016); Microfluidic Cell Culture, Second Ed. (Borenstein, Vandon, Tao & Charest, eds., Elsevier Press 2018); Human Cell Culture (Hughes, ed., Humana Press 2011); 3D Cell Culture (Koledova, ed., Humana Press 2017); Cell and Tissue Culture: Laboratory Procedures in Biotechnology (Doyle & Griffiths, eds., John Wiley & Sons 1998); Essential Stem Cell Methods, (Lanza & Klimanskaya, eds., Academic Press 2011); Stem Cell Therapies: Opportunities for Ensuring the Quality and Safety of Clinical Offerings: Summary of a Joint Workshop (Board on Health Sciences Policy, National Academies Press 2014); Essentials of Stem Cell Biology, Third Ed., (Lanza & Atala, eds., Academic Press 2013); and Handbook of Stem Cells, (Atala & Lanza, eds., Academic Press 2012). For background on microfluidic-based emulsion formation and reactions, see Niu and deMello, “Building droplet-based microfluidic systems for biological analysis”, Biochem Soc. Trans., 40:615-623 (2012); Solvas and deMello, “Droplet microfluidics: recent developments and future applications”, Chem. Commun., 47:1936-42 (2011); and Macosko, et al., Cell, 161:1202-14 (2015). CRISPR-specific techniques can be found in, e.g., Genome Editing and Engineering from TALENs and CRISPRs to Molecular Surgery, Appasani and Church (2018); and CRISPR: Methods and Protocols, Lindgren and Charpentier (2015); which is incorporated herein in its entirety by reference for all purposes.

Note that as used herein and in the appended claims, the singular forms “a,” “an,” and “the” include plural referents unless the context clearly dictates otherwise. Thus, for example, reference to “an oligonucleotide” refers to one or more oligonucleotides, and reference to “an automated system” includes reference to equivalent steps and methods for use with the system known to those skilled in the art, and so forth. Additionally, it is to be understood that terms such as “left,” “right,” “top,” “bottom,” “front,” “rear,” “side,” “height,” “length,” “width,” “upper,” “lower,” “interior,” “exterior,” “inner,” “outer” that may be used herein merely describe points of reference and do not necessarily limit embodiments of the present disclosure to any particular orientation or configuration. Furthermore, terms such as “first,” “second,” “third,” etc., merely identify one of a number of portions, components, steps, operations, functions, and/or points of reference as disclosed herein, and likewise do not necessarily limit embodiments of the present disclosure to any particular configuration or orientation.

Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. All publications mentioned herein are incorporated by reference for the purpose of describing and disclosing devices, methods and cell populations that may be used in connection with the presently described invention.

Where a range of values is provided, it is understood that each intervening value, between the upper and lower limit of that range and any other stated or intervening value in that stated range is encompassed within the invention. The upper and lower limits of these smaller ranges may independently be included in the smaller ranges, and are also encompassed within the invention, subject to any specifically excluded limit in the stated range. Where the stated range includes one or both of the limits, ranges excluding either or both of those included limits are also included in the invention.

In the following description, numerous specific details are set forth to provide a more thorough understanding of the present invention. However, it will be apparent to one of ordinary skill in the art that the present invention may be practiced without one or more of these specific details. In other instances, features and procedures well known to those skilled in the art have not been described in order to avoid obscuring the invention.

The term “complementary” as used herein refers to Watson-Crick base pairing between nucleotides and specifically refers to nucleotides hydrogen bonded to one another with thymine or uracil residues linked to adenine residues by two hydrogen bonds and cytosine and guanine residues linked by three hydrogen bonds. In general, a nucleic acid includes a nucleotide sequence described as having a “percent complementarity” or “percent homology” to a specified second nucleotide sequence. For example, a nucleotide sequence may have 80%, 90%, or 100% complementarity to a specified second nucleotide sequence, indicating that 8 of 10, 9 of 10 or 10 of 10 nucleotides of a sequence are complementary to the specified second nucleotide sequence. For instance, the nucleotide sequence 3′-TCGA-5′ is 100% complementary to the nucleotide sequence 5′-AGCT-3′; and the nucleotide sequence 3′-TCGA-5′ is 100% complementary to a region of the nucleotide sequence 5′-TAGCTG-3′.

The term DNA “control sequences” refers collectively to promoter sequences, polyadenylation signals, transcription termination sequences, upstream regulatory domains, origins of replication, internal ribosome entry sites, nuclear localization sequences, enhancers, and the like, which collectively provide for the replication, transcription and translation of a coding sequence in a recipient cell. Not all of these types of control sequences need to be present so long as a selected coding sequence is capable of being replicated, transcribed and—for some components—translated in an appropriate host cell.

As used herein the term “donor DNA” or “donor nucleic acid” or “homology arm” or “repair arm” refers to nucleic acid that is designed to introduce a DNA sequence modification (insertion, deletion, substitution) into a locus by homologous recombination using nucleic acid-guided nucleases or a nucleic acid that serves as a template (including a desired edit) to be incorporated into target DNA by reverse transcriptase in a CREATE fusion system. For homology-directed repair, the donor DNA must have sufficient homology to the regions flanking the “cut site” or the site to be edited in the genomic target sequence. The length of the homology arm(s) will depend on, e.g., the type and size of the modification being made. In many instances and preferably, the donor DNA will have two regions of sequence homology (e.g., two homology arms) to the genomic target locus. Preferably, an “insert” region or “DNA sequence modification” region—the nucleic acid modification that one desires to be introduced into a genome target locus in a cell-will be located between two regions of homology. The DNA sequence modification may change one or more bases of the target genomic DNA sequence at one specific site or multiple specific sites. A change may include changing 1, 2, 3, 4, 5, 10, 15, 20, 25, 30, 35, 40, 50, 75, 100, 150, 200, 300, 400, or 500 or more base pairs of the target sequence. A deletion or insertion may be a deletion or insertion of 1, 2, 3, 4, 5, 10, 15, 20, 25, 30, 40, 50, 75, 100, 150, 200, 300, 400, or 500 or more base pairs of the target sequence.

The terms “editing cassette”, “CREATE cassette”, “CREATE editing cassette”, or “CREATE fusion cassette” refers to a nucleic acid molecule comprising a coding sequence for transcription of a guide nucleic acid or gRNA covalently linked to a coding sequence for transcription of a donor DNA or homology arm.

The terms “guide nucleic acid” or “guide RNA” or “gRNA” refer to a polynucleotide comprising 1) a guide sequence capable of hybridizing to a genomic target locus, and 2) a scaffold sequence capable of interacting or complexing with a nucleic acid-guided nuclease.

“Homology” or “identity” or “similarity” refers to sequence similarity between two peptides or, more often in the context of the present disclosure, between two nucleic acid molecules. The term “homologous region” or “homology arm” refers to a region on the donor DNA with a certain degree of homology with the target genomic DNA sequence. Homology can be determined by comparing a position in each sequence which may be aligned for purposes of comparison. When a position in the compared sequence is occupied by the same base or amino acid, then the molecules are homologous at that position. A degree of homology between sequences is a function of the number of matching or homologous positions shared by the sequences.

“Nucleic acid-guided editing components” refers to one, some, or all of a nucleic acid-guided nuclease or nickase fusion enzyme, a guide nucleic acid and a donor nucleic acid.

“Operably linked” refers to an arrangement of elements where the components so described are configured so as to perform their usual function. Thus, control sequences operably linked to a coding sequence are capable of effecting the transcription, and in some cases, the translation, of a coding sequence. The control sequences need not be contiguous with the coding sequence so long as they function to direct the expression of the coding sequence. Thus, for example, intervening untranslated yet transcribed sequences can be present between a promoter sequence and the coding sequence and the promoter sequence can still be considered “operably linked” to the coding sequence. In fact, such sequences need not reside on the same contiguous DNA molecule (i.e., chromosome) and may still have interactions resulting in altered regulation.

A “PAM mutation” refers to one or more edits to a target sequence that removes, mutates, or otherwise renders inactive a PAM or spacer region in the target sequence.

A “promoter” or “promoter sequence” is a DNA regulatory region capable of binding RNA polymerase and initiating transcription of a polynucleotide or polypeptide coding sequence such as messenger RNA, ribosomal RNA, small nuclear or nucleolar RNA, guide RNA, or any kind of RNA. Promoters may be constitutive or inducible.

As used herein the term “selectable marker” refers to a gene introduced into a cell, which confers a trait suitable for artificial selection. General use selectable markers are well-known to those of ordinary skill in the art. Drug selectable markers such as ampicillin/carbenicillin, kanamycin, chloramphenicol, nourseothricin N-acetyl transferase, erythromycin, tetracycline, gentamicin, bleomycin, streptomycin, puromycin, hygromycin, blasticidin, and G418 may be employed. In other embodiments, selectable markers include, but are not limited to human nerve growth factor receptor (detected with a MAb, such as described in U.S. Pat. No. 6,365,373); truncated human growth factor receptor (detected with MAb); mutant human dihydrofolate reductase (DHFR; fluorescent MTX substrate available); secreted alkaline phosphatase (SEAP; fluorescent substrate available); human thymidylate synthase (TS; confers resistance to anti-cancer agent fluorodeoxyuridine); human glutathione S-transferase alpha (GSTA1; conjugates glutathione to the stem cell selective alkylator busulfan; chemoprotective selectable marker in CD34+ cells); CD24 cell surface antigen in hematopoietic stem cells; human CAD gene to confer resistance to N-phosphonacetyl-L-aspartate (PALA); human multi-drug resistance-1 (MDR-1; P-glycoprotein surface protein selectable by increased drug resistance or enriched by FACS); human CD25 (IL-2α; detectable by Mab-FITC); Methylguanine-DNA methyltransferase (MGMT; selectable by carmustine); rhamnose; and Cytidine deaminase (CD; selectable by Ara-C). “Selective medium” as used herein refers to cell growth medium to which has been added a chemical compound or biological moiety that selects for or against selectable markers.

The terms “target genomic DNA sequence”, “target sequence”, or “genomic target locus” refer to any locus in vitro or in vivo, or in a nucleic acid (e.g., genome or episome) of a cell or population of cells, in which a change of at least one nucleotide is desired using a nucleic acid-guided nuclease editing system. The target sequence can be a genomic locus or extrachromosomal locus.

The terms “transformation”, “transfection” and “transduction” are used interchangeably herein to refer to the process of introducing exogenous DNA into cells.

A “vector” is any of a variety of nucleic acids that comprise a desired sequence or sequences to be delivered to and/or expressed in a cell. Vectors are typically composed of DNA, although RNA vectors are also available. Vectors include, but are not limited to, plasmids, fosmids, phagemids, virus genomes, BACs, YACs, PACs, synthetic chromosomes, and the like. In some embodiments, a coding sequence for a nucleic acid-guided nuclease is provided in a vector, referred to as an “engine vector.” In some embodiments, the editing cassette may be provided in a vector, referred to as an “editing vector.” In some embodiments, the coding sequence for the nucleic acid-guided nuclease and the editing cassette are provided in the same vector.

Nuclease-Directed Genome Editing Generally

The compositions, methods, modules and automated instruments described herein are employed to allow one to perform nucleic acid nuclease-directed genome editing to introduce desired edits to a population of live mammalian cells. The compositions and methods entail creating reagent bundles (RBs) comprising many clonal (i.e., identical) copies of editing cassettes in a droplet formed in an immiscible fluid carrier, followed by co-localizing the RBs with live mammalian cells to effect editing of the genome of the mammalian cells by the editing cassettes.

Generally, a nucleic acid-guided nuclease or nickase fusion complexed with an appropriate synthetic guide nucleic acid in a cell can cut the genome of the live cell at a desired location. The guide nucleic acid helps the nucleic acid-guided nuclease or nickase fusion recognize and cut the DNA at a specific target sequence. By manipulating the nucleotide sequence of the guide nucleic acid, the nucleic acid-guided nuclease or nickase fusion may be programmed to target any DNA sequence for cleavage as long as an appropriate protospacer adjacent motif (PAM) is nearby. In certain aspects, the nucleic acid-guided nuclease or nickase fusion editing system may use two separate guide nucleic acid molecules that combine to function as a guide nucleic acid, e.g., a CRISPR RNA (crRNA) and trans-activating CRISPR RNA (tracrRNA). In other aspects and preferably, the guide nucleic acid is a single guide nucleic acid construct that includes both 1) a guide sequence capable of hybridizing to a genomic target locus, and 2) a scaffold sequence capable of interacting or complexing with a nucleic acid-guided nuclease or nickase fusion.

In general, a guide nucleic acid (e.g., gRNA) complexes with a compatible nucleic acid-guided nuclease or nickase fusion and can then hybridize with a target sequence, thereby directing the nuclease or nickase fusion to the target sequence. A guide nucleic acid can be DNA or RNA; alternatively, a guide nucleic acid may comprise both DNA and RNA. In some embodiments, a guide nucleic acid may comprise modified or non-naturally occurring nucleotides. Preferably and typically, the guide nucleic acid comprises RNA and the gRNA is encoded by a DNA sequence on an editing cassette along with the coding sequence for a donor DNA (e.g., whether a donor DNA to recombine with the target or a donor DNA to be reverse transcribed into the target region). Covalently linking the gRNA and donor DNA allows one to scale up the number of edits that can be made in a population of cells tremendously. Methods and compositions for designing and synthesizing editing cassettes (e.g., CREATE cassettes) are described in, e.g., U.S. Pat. Nos. 9,982,278; 10,266,849; 10,240,167; 10,351,877; 10,364,442; 10,435,715; 10,465,207; 10,669,559; 10,711,284; and 10,713,180 and U.S. Ser. Nos. 16/550,092 and 16/938,739, all of which are incorporated by reference herein. Alternatively, the nuclease or nickase fusion enzyme and gRNAs may be introduced into the cells as ribonuclease/protein complexes (RNPs), with the donor DNA introduced as an oligonucleotide or sequence to be transcribed from a vector. The donor DNA most often is introduced simultaneously with the RNPs, but may also be introduced separately from the RNPs.

A guide nucleic acid comprises a guide sequence, where the guide sequence is a polynucleotide sequence having sufficient complementarity with a target sequence to hybridize with the target sequence and direct sequence-specific binding of a complexed nucleic acid-guided nuclease or nickase fusion to the target sequence. The degree of complementarity between a guide sequence and the corresponding target sequence, when optimally aligned using a suitable alignment algorithm, is about or more than about 50%, 60%, 75%, 80%, 85%, 90%, 95%, 97.5%, 99%, or more. Optimal alignment may be determined with the use of any suitable algorithm for aligning sequences. In some embodiments, a guide sequence is about or more than about 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 40, 45, 50, 75, or more nucleotides in length. In some embodiments, a guide sequence is less than about 75, 50, 45, 40, 35, 30, 25, 20 nucleotides in length. Preferably the guide sequence is 10-30 or 15-20 nucleotides long, or 15, 16, 17, 18, 19, or 20 nucleotides in length.

In general, to generate an edit in the target sequence, the gRNA/nuclease or gRNA/nickase fusion complex binds to a target sequence as determined by the guide RNA, and the nuclease or nickase fusion recognizes a protospacer adjacent motif (PAM) sequence adjacent to the target sequence. The target sequence can be any polynucleotide endogenous or exogenous to the cell, or in vitro. For example, in the case of mammalian cells the target sequence is typically a polynucleotide residing in the nucleus of the cell. A target sequence can be a sequence encoding a gene product (e.g., a protein) or a non-coding sequence (e.g., a regulatory polynucleotide, an intron, a PAM, a control sequence, or “junk” DNA). The proto-spacer mutation (PAM) is a short nucleotide sequence recognized by the gRNA/nuclease complex. The precise preferred PAM sequence and length requirements for different nucleic acid-guided nucleases or nickase fusions vary; however, PAMs typically are 2-7 base-pair sequences adjacent or in proximity to the target sequence and, depending on the nuclease or nickase, can be 5′ or 3′ to the target sequence.

In most embodiments, genome editing of a cellular target sequence both introduces a desired DNA change to a cellular target sequence, e.g., the genomic DNA of a cell, and removes, mutates, or renders inactive a proto-spacer mutation (PAM) region in the cellular target sequence (e.g., thereby rendering the target site immune to further nuclease binding). Rendering the PAM at the cellular target sequence inactive precludes additional editing of the cell genome at that cellular target sequence, e.g., upon subsequent exposure to a nucleic acid-guided nuclease or nickase fusion complexed with a synthetic guide nucleic acid in later rounds of editing. Thus, cells having the desired cellular target sequence edit and an altered PAM can be selected for by using a nucleic acid-guided nuclease or nickase fusion complexed with a synthetic guide nucleic acid complementary to the cellular target sequence. Cells that did not undergo the first editing event will be cut rendering a double-stranded DNA break, and thus will not continue to be viable. The cells containing the desired cellular target sequence edit and PAM alteration will not be cut, as these edited cells no longer contain the necessary PAM site and will continue to grow and propagate.

As for the nuclease or nickase fusion component of the nucleic acid-guided nuclease editing system, a polynucleotide sequence encoding the nucleic acid-guided nuclease or nickase fusion can be codon optimized for expression in particular cell types, such as bacterial, yeast, and, here, mammalian cells. The choice of the nucleic acid-guided nuclease or nickase fusion to be employed depends on many factors, such as what type of edit is to be made in the target sequence and whether an appropriate PAM is located close to the desired target sequence. Nucleases of use in the methods described herein include but are not limited to Cas 9, Cas 12/CpfI, MAD2, or MAD7, MAD 2007 or other MADzymes (see U.S. Pat. Nos. 9,982,279; 10,337,028; 10,604,746; 10,665,114; 10,640,754, 10,876,102; 10,883,077; 10,704,033; 10,745,678; 10,724,021; 10,767,169; and 10,870,761 for sequences and other details related to MADzymes). Nickase fusion enzymes typically comprise a CRISPR nucleic acid-guided nuclease engineered to cut one DNA strand in the target DNA rather than making a double-stranded cut, and the nickase portion is fused to a reverse transcriptase. For more information on nickases and nickase fusion editing see U.S. Pat. No. 10,689,669 and U.S. Ser. Nos. 16/740,418; 16/740,420 and 16/740,421, both filed 11 Jan. 2020. Here, a coding sequence for a desired nuclease or nickase fusion is typically on an “engine vector” along with other desired sequences such as a selective marker.

Another component of the nucleic acid-guided nuclease or nickase fusion system is the donor nucleic acid comprising homology to the cellular target sequence and an engineered change to the cellular target sequence. For the present compositions, methods, modules and instruments the donor nucleic acid typically is in the same editing cassette as (e.g., is covalently-linked to) the guide nucleic acid and is under the control of the same promoter as the gRNA (that is, a single promoter driving the transcription of both the editing gRNA and the donor nucleic acid). The donor nucleic acid is designed to serve as a template for homologous recombination with a cellular target sequence cleaved by the nucleic acid-guided nuclease or the donor DNA serves as a template to incorporate an edit into the target via reverse transcriptase fused to a nickase as a part of the gRNA/nuclease complex. A donor nucleic acid polynucleotide may be of any suitable length, such as about or more than about 20, 25, 50, 75, 100, 150, 200, 500, or 1000 nucleotides in length, and up to 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 and up to 20 kb in length if combined with a dual gRNA architecture as described in U.S. Pat. No. 10,711,284.

In certain preferred aspects, the donor nucleic acid can be provided as an oligonucleotide of between 20-300 nucleotides, more preferably between 50-250 nucleotides. The donor nucleic acid comprises a region that is complementary to a portion of the cellular target sequence (e.g., a homology arm(s)). When optimally aligned, the donor nucleic acid overlaps with (is complementary to) the cellular target sequence by, e.g., about as few as 4 (in the case of nickase fusions) and as many as 20, 25, 30, 35, 40, 50, 60, 70, 80, 90 or more nucleotides (in the case of nucleases). The donor nucleic acid typically comprises two homology arms (regions complementary to the cellular target sequence) flanking the mutation or difference between the donor nucleic acid and the cellular target sequence, although in CREATE fusion embodiments, the edit may be located at one end of a single homology arm rather than positioned between two homology arms. The donor nucleic acid comprises at least one mutation or alteration compared to the cellular target sequence, such as an insertion, deletion, modification, or any combination thereof compared to the cellular target sequence.

As described in relation to the gRNA, the donor nucleic acid is provided as part of a rationally-designed editing cassette along with a promoter to drive transcription of both the gRNA and donor DNA. As described below, the editing cassette may be provided as a linear editing cassette, or the editing cassette may be inserted into an editing vector. Moreover, there may be more than one, e.g., two, three, four, or more editing gRNA/donor nucleic acid pair rationally-designed editing cassettes linked to one another in a linear “compound cassette” or inserted into an editing vector; alternatively, a single rationally-designed editing cassette may comprise two to several editing gRNA/donor DNA pairs, where each editing gRNA is under the control of separate different promoters, separate promoters, or where all gRNAs/donor nucleic acid pairs are under the control of a single promoter. In some embodiments the promoter driving transcription of the editing gRNA and the donor nucleic acid (or driving more than one editing gRNA/donor nucleic acid pair) is an inducible promoter. In many if not most embodiments of the compositions, methods, modules and instruments described herein, the editing cassettes make up a collection or library editing gRNAs and of donor nucleic acids representing, e.g., gene-wide, pathway-wide or genome-wide libraries of editing gRNAs and donor nucleic acids.

In addition to the donor nucleic acid, the editing cassettes comprise one or more primer binding sites to allow for PCR amplification of the editing cassettes. The primer binding sites are used to amplify the editing cassette by using oligonucleotide primers and may be biotinylated or otherwise labeled. In addition, the editing cassette may comprise a barcode. A barcode is a unique DNA sequence that corresponds to the donor DNA sequence such that the barcode serves as a proxy to identify the edit made to the corresponding cellular target sequence. The barcode typically comprises four or more nucleotides. Also, in preferred embodiments, an editing cassette or editing vector or engine vector further comprises one or more nuclear localization sequences (NLSs), such as about or more than about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more NLSs.

Mammalian Cell Growth, Reagent Bundle Creation Transformation and Editing

The present compositions and methods are drawn to nucleic acid-guided nuclease editing of live mammalian cells. The methods involve creating reagent bundle droplets comprising hundreds of thousands to millions of clonal copies of an editing cassette in each RB. A library of RB s comprises hundreds to thousands to tens of thousands of different editing cassettes; thus, the methods are scalable for delivering hundreds, thousands, tens of thousands or more different editing cassettes to a population of live cells. Once the library of RBs is created, the methods include delivering or co-localizing the RBs with the live mammalian cells, transfecting the cells and finally culturing the edited cells.

In the present methods, mammalian cells are often grown in culture for several passages before entry into an automated process. Cell culture is the process by which cells are grown under controlled conditions, almost always outside the cell's natural environment. For mammalian cells, culture conditions typically vary somewhat for each cell type but generally include a medium and additives that supply essential nutrients such as amino acids, carbohydrates, vitamins, minerals, growth factors, hormones, and gases such as, e.g., O₂ and CO₂. In addition to providing nutrients, the medium typically regulates the physio-chemical environment via a pH buffer, and most cells are grown at 37° C. Many mammalian cells require or prefer a surface or artificial substrate on which to grow (e.g., adherent cells), whereas other cells such as hematopoietic cells and some adherent cells can be grown in or adapted to grow in suspension. Adherent cells often are grown in 2D monolayer cultures in petri dishes or flasks, but some adherent cells can grow in suspension cultures to higher density than would be possible in 2D cultures. “Passages” generally refers to transferring a small number of cells to a fresh substrate with fresh medium, or, in the case of suspension cultures, transferring a small volume of the culture to a larger volume of medium.

Mammalian cells include primary cells, which are cultured directly from a tissue and typically have a limited lifespan in culture; established or immortalized cell lines, which have acquired the ability to proliferate indefinitely either through random mutation or deliberate modification such as by expression of the telomerase gene; and stem cells, of which there are undifferentiated stem cells or partly-differentiated stem cells that can both differentiate into various types of cells and divide indefinitely to produce more of the same stem cells.

Primary cells can be isolated from virtually any tissue. Immortalized cell lines can be created or may be well-known, established cell lines such as human cell lines DU145 (derived from prostate cancer cells); H295R (derived from adrenocortical cancer cells); HeLa (derived from cervical cancer cells); KBM-7 (derived from chronic myelogenous leukemia cells); LNCaP (derived from prostate cancer cells); MCF-7 (derived from breast cancer cells); MDA-MB-468 (derived from breast cancer cells); PC3 (derived from prostate cancer cells); SaOS-2 (derived from bone cancer cells); SH-SY5Y (derived from neuroblastoma cells); T-047D (derived from breast cancer cells); TH-1 (derived from acute myeloid leukemia cells); U87 (derived from glioblastoma cells); and the National Cancer Institute's 60 cancer line panel NCI60; and other immortalized mammalian cell lines such as Vero cells (derived from African green monkey kidney epithelial cells); the mouse line MC3T3; rat lines GH3 (derived from pituitary tumor cells) and PC12 (derived from pheochromocytoma cells); and canine MDCK cells (derived from kidney epithelial cells).

Stem cells are of particular interest in the methods and compositions described herein. Generally speaking, there are three general types of mammalian stem cells: adult stem cells (ASCs), which are undifferentiated cells found living within specific differentiated tissues including hematopoietic, mesenchymal, neural, and epithelial stem cells; embryonic stem cells (ESCs), which in humans are isolated from a blastocyst typically 3-5 days following fertilization and which are capable of generating all the specialized tissues that make up the human body; and induced pluripotent stem cells (iPSCs), which are adult stem cells that are created using genetic reprogramming with, e.g., protein transcription factors.

Once the cells of choice have been grown and passaged several times—in some embodiments off-instrument—in a first step the mammalian cells that are to be edited are transferred to an automated instrument where the cells are grown in cell culture and the growth of the cells is monitored. Monitoring is usually performed by imaging the cells as described infra and/or by, e.g., measuring pH of the medium using a medium comprising a pH indicator. As opposed to 2D culture of cells as described above, the present methods envision culturing the cells in suspension. Growing cells in suspension can be effected in various forms. Adherent cells that typically are grown in 2D cultures when grown in suspension often aggregate into “clumps.” For example, some iPSCs grow well as aggregates in suspension, and are most healthy growing in aggregates of 50-300 microns in size, starting off as smaller aggregates 30-50 microns in size. iPSCs are typically grown in culture 3-5 days between passaging and the larger aggregates are broken into smaller aggregates by filtering them, e.g., through a cell strainer (e.g., a sieve) with a 37 micron filter. The iPSCs can grow indefinitely in 3D aggregates as long as they are passaged into smaller aggregates when the aggregates become approximately 300-400 microns in size.

An alternative to growing cells in 3D aggregates is growing cells on microcarriers. Generally, microcarriers are nonporous (comprised of pore sizes range from 0-20 nm), microporous (comprised of pore sizes range from 20 nm-1 micron), and macroporous (comprised of pore sizes range from 1-50 microns) microcarriers comprising natural organic materials such as, e.g., gelatin, collagen, alginate, agarose, chitosan, and cellulose; synthetic polymeric materials such as, e.g., polystyrene, polyacrylates such as polyacrylamide, polyamidoamine (PAMAM), polyethylene oxide (PEO/PEG), poly(N-isopropylacrylamide) (PNIPAM), polycaprolactone (PCL), polylactic acid (PLA), and polyglycolic acid (PGA); inorganic materials such as, e.g., silica, silicon, mica, quartz and silicone; as well as mixtures of natural, polymeric materials, cross-linked polymeric materials, and inorganic materials etc. on which animal cells can grow. Microcarriers useful in the methods herein typically range in size from 30-1200 microns in diameter and more typically range in size from 40-200 or from 50-150 microns in diameter.

Finally, another option for growing mammalian cells for editing in the compositions, methods, modules and automated instruments described herein is growing single cells in suspension using a specialized medium such as that developed by ACCELLTA™ (Haifa, Israel). Cells grown in this medium must be adapted to this process over many cell passages; however, once adapted the cells can be grown to a density of >40 million cells/ml and expanded 50-100× in approximately a week, depending on cell type.

There are three exemplary modules—as an alternative to classic culture in flasks or plates—for growing and monitoring cells off-instrument or in the automated instruments described herein. One module is a rotating growth module, which is depicted in FIGS. 3A-3E, another module is a tangential flow filtration module, which is depicted in FIGS. 4A-4G and finally another module is a bioreactor, features of which are depicted in FIGS. 5A-5I. These modules can be adapted to dissociate cells (if required) as well and are described in detail in relation to these figures. The cells grown off-instrument or in a growth module of the automated instrument as well as reagents needed for cell growth, nucleic acid amplification, cell transfection or transduction, cell editing and enrichment may be provided in a reagent cartridge. The cells and reagents are moved from the reagent cartridge and between modules by a robotic liquid handling system including the gantry. As an example, the robotic liquid handling system may include an automated liquid handling system such as those manufactured by Tecan Group Ltd. of Mannedorf, Switzerland, Hamilton Company of Reno, Nev. (see, e.g., WO2018015544A1 to Ott, entitled “Pipetting device, fluid processing system and method for operating a fluid processing system”), or Beckman Coulter, Inc. of Fort Collins, Colo. (see, e.g., US20160018427A1 to Striebl et al., entitled “Methods and systems for tube inspection and liquid level detection”), and typically includes an air displacement pipettor.

Reagent cartridges, such as those described in U.S. Pat. No. 10,376,889; 10,406,525; 10,478,222; 10,576,474; 10,639,637 and 10,738,271 allow for particularly easy integration with liquid handling instrumentation. In some embodiments, only the air displacement pipettor is moved by the gantry and the various modules and reagent cartridge remain stationary. In alternative embodiments, an automated mechanical motion system (actuator) additionally supplies XY axis motion control or XYZ axis motion control to one or more modules and/or cartridges of the automated multi-module cell processing system. Used pipette tips, for example, may be placed by the robotic handling system in a waste repository. For example, an active module may be raised to come into contact-accessible positioning with the robotic handling system or, conversely, lowered after use to avoid impact with the robotic handling system as the robotic handling system is moving materials to other modules within the automated multi-module cell processing instrument. Alternatively, the cells may be transferred to the growth module by the user.

Alternatively, in some embodiments, a gantry and/or an air displacement pump is not used; instead, in one embodiment reagents are individually connected to the bioreactor, typically via tubing or microfluidic circuits; in another embodiment, reagents may be connected to a manifold that has a single connection to the bioreactor. In some embodiments, the bioreactor is a completely closed fluidic system; that is, e.g., no pipets piercing reagent tubes and transferring liquid.

In a next step, the cells that have been grown in suspension or on microcarriers are dissociated or, if grown on microcarriers, may be dissociated from the microcarrier and/or transferred to fresh microcarriers. Dissociation is required if the cells grown as cell aggregates. In one embodiment, dissociation may be via mechanical means such as agitation or by a filter, frit or sieve. Such a filter, frit or sieve may be adapted to be part of the rotating growth module, tangential flow filtration module, or bioreactor module as described in relation to FIGS. 3A-3E, 4A-4E, and 5A-5I or may be a separate “dissociation only module.” As an alternative, aggregates of cells may be dissociated by enzymes such as hemagglutinin, collagenase, dispase and trypsin, which can be added to the medium of the growing cells in the rotating growth module, tangential flow filtration module or bioreactor. If the cells are grown on microcarriers, the cells can be dissociated from the microcarriers using enzymes that are typically used in cell culture to dissociate cells in 2D culture, such as collagenase, trypsin or pronase or by non-enzymatic methods including EDTA or other chelating chemicals. In a bioreactor, dissociation can be performed mechanically using, e.g., an impeller or enzymatically, or cells grown in a bioreactor may be transferred to a dissociation module.

In parallel with growing and preparing the cells for transfection, reagent bundles (RBs) are created and once the cells have been dissociated, the reagent bundles and cells are co-localized. The RBs (droplets) comprise thousands to millions of clonal copies of an editing cassette—either RNA or DNA editing cassettes and in various configurations, e.g., dsDNA, ssDNA, ssRNA, linear or circular templates.

Finally, in some methods and instruments, the population of cells after editing are enriched for edited cells by, e.g., magnetic beads, antibiotic selection, co-edit selection, or FACS sorting, all of which are described in detail infra.

Liquid Droplet Reagent Delivery for Editing Cells Grown in Suspension

FIG. 1A depicts an exemplary workflow employing liquid-partitioned (e.g., droplet) delivery for editing mammalian cells grown in suspension. In this exemplary embodiment, microfluidic droplet generation is used to clonally amplify editing cassettes or editing vectors used to transform or transfect mammalian cells. Microfluidic droplet generation using two immiscible fluids (e.g., an aqueous solution and an oil) that meet at intersecting microchannels with droplets being generated at a junction between the two microfluidic channels has been known in the art for several decades. The terms “droplet” and “emulsion” are used interchangeably herein to refer to an aliquot of one fluid (here, an aqueous solution) in an immiscible carrier fluid (e.g., an oil), with the carrier fluid substantially surrounding the aqueous droplet. (See FIG. 1B.) For example, in 1984 Shaw Stewart taught the use of a device to produce microfluidic emulsion droplets from two immiscible fluids that meet at an intersecting channel. (UK Patent Application No. 2097692 to Shaw Stewart.) Shaw Stewart introduced the concept of a microfluidic “T-junction” at which droplets of an aqueous solution can be formed using a continuously flowing immiscible “carrier phase.” By the 1990s, various groups were looking to both miniaturize and automate biological and chemical reactions and by the early 2000s research groups had shown proof of principle for the use of aqueous droplets in an oil carrier for carrying out various analyses, cell sorting operations and biochemical reactions including PCR. (See, e.g., US Pub. No. 2002/0058332 to Quake, et al.)

The immiscible fluids used in the microchannels may be provided by on-chip wells or off-chip reservoirs and the channels intersect as T-junctions to form the droplets. A pressure differential is used to control the flow of the fluids at the T-junction, shearing-off of the aqueous fluid into the immiscible oil flow to create droplets. By adjusting the pressure of the flowing fluids, a pressure difference can be established to shear off droplets of the aqueous solution at a regular frequency as the aqueous solution enters the oil stream, thereby forming droplets in the oil stream. The droplets optionally may be combined with other droplets to effect a reaction between the reactants when the droplets combine.

In the 2000s a “cross junction” strategy was introduced. In the cross-junction approach, aqueous droplets are formed at converging flows of the immiscible fluids where a continuous phase (here, the oil phase) where the converging flows “pinch” off the droplets of the aqueous phase at a droplet-forming junction. This “flow focusing” approach, in which the aqueous droplet is focused by the oil phase at the cross junction, is described, for example, by Higuchi, et al. (US Pat. Pub. 2004/0068019) (See, e.g., FIG. 1B infra.) Microfluidic devices or “chips” are available commercially through, e.g., microfluidic ChipShop™ GmbH (Jena, Germany); uFluidix™ (Toronto, Canada); Microflexis™ (Hamburg, Germany); and microLIQUID™ (Gipuzkoa, Spain).

The present embodiment using droplets is particularly useful in providing discretely-apportioned “mini reactors” and for co-partitioning reagents with cells for further reaction and analysis. Co-partitioning of reagents and sample components can be used, for example, for reducing the complexity of sample material by segregating portions of the sample into different partitions. As with the gel beads described infra, by segregating reagents each sample portion (e.g., cell or group of cells) can be subjected into a different reaction with thousands, tens of thousands, hundreds of thousands or more reactions taking place in parallel.

Further in the case of droplets in an emulsion, allocating individual molecules (e.g., Poisson distribution of molecules in droplets) is accomplished by introducing an aqueous stream of fluid comprising the molecules into a flowing stream of a carrier fluid such that droplets are generated at the junction of the two streams. By providing the aqueous molecule-containing (or cell-containing) stream at a certain concentration level, the number of droplets containing molecules (or cells) can be controlled. In the present methods, it is desirable to control the relative flow rates of the aqueous and non-aqueous fluid such that, on average, the droplets contain less than one molecule per droplet to ensure that any one droplet will comprise either one molecule or no molecule. Thus, the droplet method (or gel bead method) allows one to partition a single editing cassette construct, amplify the single copy to make thousands, tens of thousands, hundreds of thousands or more copies for delivery as opposed to the other method of pooling editing cassettes, amplifying the pooled editing cassettes and then de-multiplexing the pool of amplified editing cassettes. Both methods, however, result in RBs with hundreds of thousands to millions of clonal copies of editing cassettes in or on a partition (e.g., droplet, gel bead or microcarrier).

In addition, cell sorting may be performed on a microfluidic device. While conventional methods can provide high efficiency sorting in short timescales, advances in microfluidics have enabled the realization of miniaturized devices offering similar capabilities that exploit a variety of physical principles. These technologies may be classified as either active or passive. Active systems generally use external fields (e.g., acoustic, electric, magnetic, and optical) to impose forces to displace cells for sorting; whereas passive systems use inertial forces, filters, and adhesion mechanisms to purify cell populations. Cell sorting on microchips provides numerous advantages over conventional methods by reducing the size of necessary equipment, eliminating potentially biohazardous aerosols, and simplifying the complex protocols commonly associated with cell sorting. Further, microchip devices are well suited for parallelization, enabling complete lab-on-a-chip devices for cellular isolation, analysis, and experimental processing. Cell sorting on microchips includes label-based sorting, detectable by electrokinetic mechanisms such as, e.g., electrophoresis and dielectric phoresis; acoutstrophoresis; optical sorting; mechanical systems; bead-based sorting via, e.g., magnetophoresis and electrokinetic mechanisms; and label-free cell sorting via, e.g., acoustophoresis and optical switching mechanisms. Cell sorting in microfluidics devices is discussed in, e.g., Shields, et al., Microfluidic Cell Sorting: A Review of the Advances in the Separation of Cells from Debulking to Rare Cell Isolation, Lab Chip, 15(5):1230-49 (2015); and U.S. Pub. Nos. 2015/0268244; 2008/0213821; 2020/0190488; and 2005/0164158.

FIG. 1A shows that the liquid droplet workflow begins with cell culture, typically off-instrument. Again, the cells may be grown off-instrument in 2D culture in plates or tissue culture flasks, or in 3D culture (if the cells are viable when grown in or adapted to 3D culture) on microcarriers in spinner flasks or in a bioreactor as described herein infra. As described previously, if necessary, the cells are dissociated and added to medium in an on-instrument growth module such as, e.g., a rotating growth vial, TFF reservoir or bioreactor comprising cell growth medium such as DMEM. If the cells are grown initially on cell growth microcarriers, the microcarriers are transferred to a rotating growth vial or TFF reservoir or bioreactor comprising cell growth medium such as MEM, DMEM or the like and additional microcarriers. Alternatively, single cells may be grown in suspension using the specialized medium developed by ACCELLTA™ (Haifa, Israel); however, cells grown in this medium must be adapted to this process. Once grown, approximately 1e7 cells are transferred to the automated instrument for growth. The cells are grown in 3D culture in aggregates or on microcarriers in the RGV, TFF or bioreactor for, e.g., three days or until a desired number of cells, e.g., 1e8 cells are present. During this growth cycle, the cells are monitored for cell number, pH, and optionally other parameters.

Cell dissociation, if required, is performed by removing cells from cell growth microcarriers using enzymes such as collagenase, trypsin or pronase, or by non-enzymatic methods including EDTA or other chelating chemicals, and then passing cell aggregates through a filter, frit or sieve by agitating the cells or if grown in suspension as aggregates simply by passing the aggregates through a filter or sieve, or by treatment with, e.g., hemagluttinin. Alternatively, and as described in relation to FIG. 5D and Examples VIII and IX, cells grown on microcarriers in a bioreactor can be detached and dissociated using an impeller, which creates turbulence in the medium in which the cells are grown. In addition, combination of these techniques may be used.

In the embodiments described herein, reagents are “packaged” and delivered to the cells via a microfluidic device, described in detail infra with reference to FIGS. 1B and 1C, and editing takes place in droplets on the microfluidic device as well. FIG. 1B depicts a microfluidic channel structure 100 for the flow focusing or partitioning of individual molecules in droplets. The channel structure 100 includes channel sections 102, 104, 106 and 108 all joined at channel junction 110. In operation, an aqueous fluid 112—here, e.g., a buffer comprising PCR reagents (e.g., primers, enzyme, dNTPs) that includes CREATE editing cassettes 114 at a concentration determined to allow formation of droplets comprising no editing cassette or one editing cassette—is transported along channel section 102 into channel junction 110, while a second fluid 116 that is immiscible with aqueous fluid 112 is delivered to channel junction 110 from channel sections 104 and 106 to create droplets 118 and 120. In the present example, the concentration of editing cassettes is such that at droplet formation, some droplets contain an editing cassette while some droplets do not. Such a Poisson distribution of editing cassettes in droplets allows for clonal amplification of editing cassettes in the droplets where each droplet then comprises many copies of a single editing cassette or no editing cassettes. Channel section 108 may be fluidically coupled to an outlet reservoir into which the droplets may be stored.

The droplets comprising the editing cassettes and PCR reagents described herein are characterized by having extremely small volumes, e.g., approximately equal to or less than 10 nL (and as low as 0.1 nL), approximately equal to or less than 5 nL, approximately equal to or less than 2 nL, approximately equal to or less than 1 nL, approximately equal to or less than 900 picoliters (pL), approximately equal to or less than 800 pL, approximately equal to or less than 700 pL, approximately equal to or less than 600 pL, approximately equal to or less than 500 pL, approximately equal to or less than 400 pL, approximately equal to or less than 300 pL, approximately equal to or less than 200 pL, approximately equal to or less than 100 pL, approximately equal to or less than 50 pL, approximately equal to or less than 25 pL, approximately equal to or less than 10 pL, approximately equal to or less than 5 pL, approximately equal to or less than 1 pL, approximately equal to or less than 500 nanoliters (fL), approximately equal to or less than 100 fL, approximately equal to or less than 50 fL, or even less.

The fluid that is immiscible with the aqueous fluid is typically a non-polar hydrophobic fluid such as an oil, e.g., mineral oil, or an organic liquid such as hexadecane. Fluorinated oils are commonly used, with a fluorosurfactant added to stabilize the droplets that are formed. Non-limiting examples of fluorophilic components that can be used in either a surfactant and/or a continuous phase include: perfluorodecalin, perfluoromethyldecalin, perfluoroindane, perfluorotrimethyl bicyclo[3.3.1]nonane, perfluoromethyl adamantine, perfluoro-2,2,4,4-tetra-methylpentane; 9-12C perfluoro amines, e.g., perfluorotripropyl amine, perfluorotributyl amine, perfluoro-1-azatricyclic amines; bromofluorocarbon compounds, e.g., perfluorooctyl bromide and perfluorooctyl dibromide; F-4-methyl octahydroquinolidizine and perfluoro ethers, including chlorinated polyfluorocyclic ethers, perfluoro-4-methylmorpholine, perfluorotriethylamine, perfluoro-2-ethyltetrahydrofuran, perfluoro-2-butyltetrahydrofuran, perfluoropentane, perfluoro(2-methylpentane), perfluorohexane, perfluoro-4-isopropylmorpholine, perfluorodibutyl ether, perfluoroheptane, perfluorooctane, perfluorotripropylamine, perfluorononane, perfluorotributylamine, perfluorodihexyl ether, perfluoro [2-(diethylamino)ethyl-2-(N-morpholino)ethyl]ether, n-perfluorotetradecahydrophenanthrene, and mixtures thereof.

Generally, the channel sections are coupled to different fluid sources, receiving and/or output reservoirs, tubing, manifolds, compressors, pumps, vacuums, actuators or other flow controls. For exemplary microfluidic droplet generators and methods, see, e.g., U.S. Pat. Nos. 8,822,148; 8,304,193; 8,889,083; 9,216,392; 9,347,059; 9,089,844; 9,126,160; 9,500,664; 9,636,682; and 9,649,635; and US Pub. Nos. 2010/0105122; 2014/0155295; 2018/0312873; 2019/0176152; and 2019/0233878.

In the present methods, the “payload” for the droplets is an editing cassette construct, again where the vast majority of beads comprise one or no editing cassette construct. As described above, an editing cassette (e.g., CREATE cassette or CREATE fusion cassette) comprises a coding sequence for transcription of a guide nucleic acid or gRNA covalently linked to a coding sequence for transcription of a donor DNA (whether configured for nuclease or nickase fusion (e.g., CREATE fusion) editing) and an editing cassette construct further comprises the editing cassette linked to a promoter to drive transcription of the gRNA and donor DNA. Covalently linking the gRNA and donor DNA allows one to scale up the number of edits that can be made simultaneously in a population of cells tremendously. In addition to the promoter, coding sequence for transcription of the gRNA and coding sequence for transcription of the donor DNA, the editing cassette construct may comprise other functional elements that are used in processing (e.g., amplification) of the editing cassette sequences, including, e.g., primer sequences (targeted or universal, preferably in most embodiments herein, universal), labels, enrichment sequences, immobilization sequences, barcodes, and NLSs. (See, e.g., FIG. 11.) The editing cassette construct can be, depending on the embodiment, a linear construct, a circular construct, a double-stranded construct or single-stranded construct and comprise DNA, RNA, nucleic acid mimetics of a combination thereof.

FIG. 1C depicts an exemplary method for transforming and editing live mammalian cells via nucleic acid-guided nuclease or nickase fusion editing using the concept depicted in FIG. 1B. The method depicted in FIG. 1C begins, at top left, with a pool of CREATE editing cassette constructs. The pool of editing cassettes is diluted in an aqueous solution comprising amplification reagents (e.g., dNTPs, primers and polymerase enzyme) and introduced into a microfluidic droplet generator device where aqueous droplets comprising a Poisson distribution of editing cassette constructs are generated, such as seen in FIG. 1B. In the presence of the amplification reagents, the editing cassette constructs in the droplets comprising editing cassette constructs are amplified, creating clonal copies of the editing cassette constructs confined to the droplets. In the droplets that did not receive an editing cassette, there should be no amplification. Thermocycling is provided if PCR is performed as opposed to isothermal amplification.

The editing cassette constructs, the primers or dNTPs used to amplify the editing cassette constructs may comprise a label, such as a fluorescent or chemiluminescent label, which labels the amplicons as they are produced. In certain cases, the detectable label is a fluorophore, which, after absorption of energy, emits radiation at a defined wavelength. Fluorescent detectable labels include, for example, dansyl-functionalized fluorescent moieties (see, e.g., Welch et al., Chem. Eur. J. 5(3):951-960 (1999)); and fluorescent labels Cy3 and Cy5 (see, e.g., Zhu et al., Cytometry 28:206-211 (1997)). Detectable labels are also disclosed in Prober et al., Science 238:336-341 (1987); Connell et al., BioTechniques 5(4):342-384 (1987); Ansorge et al., Nucl. Acids Res. 15(11):4593-4602 (1987) and Smith et al., Nature 321:674 (1986). Other commercially available fluorescent labels include, but are not limited to, fluorescein, rhodamine (including TMR, Texas red and Rox), alexa, bodipy, acridine, coumarin, pyrene, benzanthracene and the cyanins.

Following PCR, the droplets are, e.g., FACS sorted where droplets comprising amplified editing cassette constructs are segregated from droplets that do not contain amplified editing cassette constructs. This process is shown in FIG. 1C at top right. For sorting, the droplets may be sorted suspended in the oil carrier or the droplets in the oil carrier may be further dispersed in an aqueous phase—creating a double emulsion—for sorting.

Once sorted, the segregated droplets comprising the amplified editing cassette constructs can then be introduced into a stream of carrier fluid comprising aqueous droplets containing, e.g., transformation, transfection or transduction reagents such as, for example, lipofection, nucleofection, biolistic, virosome, liposome, immunoliposome, polycation or lipid:nucleic acid conjugate reagents. The step of combining or coalescing droplets comprising amplified editing cassettes and droplets comprising lipofection reagents is depicted in FIG. 1C at bottom left. The droplets comprising the amplified editing cassettes and transformation or transfection reagents are coalesced in the microfluidic device using one of several methods that may be used to cause coalescence of droplets. Such methods include providing a localized electric field to coalesce the droplet, providing locally a chemical that disrupts or destabilizes the surfactant in the continuous phase, such as, e.g., perfluoro-octanol, or use of a textured surface in the flow path of the microfluidic channel as described in US Pub. No. 2019/0176152.

Following coalescence of the amplified editing cassette constructs and transformation or transfection reagents into single partitions, droplets or “reagent bundles”, the reagent bundles may then be introduced into a stream of aqueous droplets comprising one or more cells in each droplet. This process is depicted in FIG. 1C at bottom right. Again, the cells are grown on-instrument in one of the three growth modules described infra. In this step, the reagent bundles are coalesced with the droplets comprising cells to effect transfection of the editing cassette constructs into cells. Once sufficient time for transfection has occurred, for example, from 1 minute to 24 hours, or from 2 minutes to 12 hours, or from 5 minutes to 8 hours, or from 7 minutes to 4 hours, or from 10 minutes to 2 hours, the droplets containing the cells and reagent bundles can be demulsified, and the cells are allowed to continue to grow in an appropriate medium or the cells optionally are washed and plated or washed and cultured in 3D culture in an appropriate medium (e.g., on microcarriers in the RGV, TFF or bioreactor) which allows the cells to recover and grow.

In the embodiment shown in FIG. 1C (and in FIG. 1D), a vector comprising the coding sequence for the nuclease has already been transformed or transfected into the cells prior to dispersing the cells in droplets in an oil carrier. However, in alternative embodiments, the nuclease may be integrated into the genome of the cells to be edited or a coding sequence for the nuclease or nuclease fusion (either as a linear construct or as part of an engine vector) or the nuclease or nuclease fusion protein itself may be provided in droplets with the transformation or transfection reagents and transfected into the cells concurrently with the amplified editing cassettes.

Solid Wall Partitioned Delivery for Editing Cells Grown in Suspension

FIG. 2A depicts an exemplary workflow employing solid wall partitioning and editing of mammalian cells grown in suspension. Again, the cells may be grown off-instrument in 2D culture in plates or tissue culture flasks, or in 3D culture (if the cells are viable when grown in or adapted to 3D culture) on microcarriers in spinner flasks or in a bioreactor as described herein infra. As described previously, if the cells are initially grown in 2D or 3D culture, the cells are dissociated and added to medium in, e.g., a rotating growth vial, TFF reservoir or bioreactor comprising cell growth medium or SWIIN reservoir 652 in FIG. 6A. The overall work flow for cell growth in SWIIN comprises loading a cell culture to be grown into a reservoir 652, preferably bubbling air or an appropriate gas through the cell culture, passing or flowing the cell culture to reservoir 654 by modifying reservoir seal 662 into a connection channel, optionally adding additional fresh or different medium to the cell culture and optionally bubbling air or gas through the cell culture, then repeating the process, all while measuring, e.g., the optical density of the cell culture in the reservoirs continuously or at desired intervals. Again, cell growth monitoring can be performed by imaging, for example, by allowing the microcarriers to settle and imaging the bottom of the SWIIN reservoir. Alternatively, an aliquot of the culture is removed and run through a flow cell for imaging.

In yet another alternative, the cells may express a fluorescent protein and fluorescence is measured. In an alternative approach, reservoir seal 662 is modified into a connection channel containing a filter, frit or sieve for passaging large cell aggregates into smaller aggregates or clumps.

If the cells are grown initially on microcarriers, the microcarriers are transferred to a rotating growth vial, TFF reservoir, or bioreactor comprising cell growth medium and, optionally, additional microcarriers comprising cell growth medium and additional microcarriers. Alternatively, single cells may be grown in suspension using the specialized medium developed by ACCELLTA™ (Haifa, Israel). Once grown, approximately 1e7 cells are transferred to the automated instrument for growth. During this growth cycle, the cells are monitored for cell number, pH, and optionally other parameters. Cell dissociation, if required, is performed by removing cells from microcarriers using enzymes such as collagenase, trypsin or pronase, or by non-enzymatic methods including EDTA or other chelating chemicals, and then passing cell aggregates through a filter, frit or sieve or by using another mechanical means such as an impeller or other agitation means.

In this embodiment, like the liquid droplet embodiment, reagents are “packaged” in a microfluidic device; however, unlike the liquid droplet embodiment, reagents are delivered to the cells in a solid wall device. Thus, the cells, once grown on-instrument and dissociated, are dispensed into microwells, such as the solid wall isolation, incubation, and normalization (SWIIN) device depicted in FIGS. 6A-6D and described in detail below, such that each well or partition (in some embodiments, at least 100,000 partitions) comprises approximately 250 to 1500 cells, or from 500 to 1000 cells. Exemplary processes for forming gel beads are described in relation to FIG. 2B-2D infra.

FIG. 2B depicts an exemplary method for encapsulating reagent bundles comprising amplified editing cassette constructs in gel beads. At top of FIG. 2B, an aqueous solution comprising PCR reagents is flowed through a channel 202, and an aqueous solution comprising editing cassette constructs 212 at a dilution pre-determined to provide droplets with one or no editing cassette is flowed through a channel 204 that intersects the channel with the PCR reagents (e.g., enzyme, primers and dNTPs) 202. The channel with the combined editing cassette constructs and PCR reagents is then flow-focused by two converging streams (from channels 206 and 208) of an oil carrier, thereby forming droplets of PCR reagents and editing cassette constructs 218 or droplets containing PCR reagents only 220. At bottom of FIG. 2B shows a droplet 218 comprising PCR reagents and an editing cassette construct 212. In a next step, the droplet is polymerized to form a gel bead or gel matrix 222. In some embodiments, a gel bead can create a system comprising a large molecule such as an editing cassette construct within the boundary of the gel bead, while allowing small molecules such as enzymes dNTPs, primers and, e.g., lipoplex, to permeate the matrix. Further, the gel bead may comprise a labile bond such that after the gel bead is degraded, the large molecule is released from the gel matrix.

In some of the embodiments herein—such as the method depicted in this FIG. 2B—the editing cassette constructs, nuclease or nickase fusion coding sequence, engine vector, PCR reagents, transformation or transfection reagents, etc. are encapsulated in gel beads during gel bead generation (e.g., during polymerization of precursors). In other embodiments, small molecules such as lipofect or PCR reagents (e.g., primers, polymerases, dNTPs, co-factors) and buffers may be added to the gel beads after formation. Alternatively, the polymer network may be chemically modified to conjugate specifically with a target molecule for retention. Encapsulated reagents and molecules may be released from a gel bead upon degradation of the gel bead.

Looking again at FIG. 2B, following polymerization (e.g., formation) of the gel bead, amplification of editing cassette constructs 212 takes place inside the gel bead 224. Alternatively, however, amplification of the editing cassette constructs 212 may take place before gel bead polymerization; that is, the amplification take place in the droplet before polymerization into a gel bead.

FIG. 2C is similar to FIG. 1C at top; however, in FIG. 2C the editing cassettes, PCR reagents and transfection reagents are combined into a gel bead rather than retained within a droplet. The method depicted in FIG. 2C begins—like the method depicted in FIG. 1B—with a pool of editing cassette constructs in an aqueous solution comprising PCR reagents and, here, transfection reagents. The pool of editing cassettes and reagents is introduced into a microfluidic droplet generator device such as those described supra where aqueous droplets comprising a Poisson distribution of editing cassette constructs are generated. Here, however, the generated aqueous droplets are subsequently polymerized into gel beads. Once the gel beads are formed, the editing cassette constructs in the gel beads are amplified thereby creating clonal copies of the editing cassette constructs in the gel beads. Again, in the droplets that did not receive an editing cassette construct, there should be no amplification. As with the method depicted in FIG. 1C, the editing cassette constructs, primers used to amplify the editing cassette constructs or dNTPs may comprise a label, such as a fluorescent or chemiluminescent label, which labels the amplicons. Once amplification has taken place the gel beads are demulsified (e.g., removed from the carrier fluid by washing or methods such as chemical destabilization, mechanical rupture, or electrocoalescence) and are sorted to separate the editing cassette construct-containing gel beads from the gel beads that did not receive an editing cassette during droplet formation.

Again, cell sorting on microfluidic devices has been accomplished by several different technologies, generally classified as either active or passive. Active systems generally use external fields (e.g., acoustic, electric, magnetic, and optical) to impose forces to displace cells for sorting; whereas passive systems use inertial forces, filters, and adhesion mechanisms to purify cell populations. Cell sorting on microchips provides numerous advantages over conventional methods by reducing the size of necessary equipment, eliminating potentially biohazardous aerosols, and simplifying the complex protocols commonly associated with cell sorting. Further, microchip devices are well suited for parallelization, enabling complete lab-on-a-chip devices for cellular isolation, analysis, and experimental processing. Cell sorting on microchips includes label-based sorting, detectable by electrokinetic mechanisms such as, e.g., electrophoresis and dielectric phoresis; acoutstrophoresis; optical sorting; mechanical systems; bead-based sorting via, e.g., magnetophoresis and electrokinetic mechanisms; and label-free cell sorting via, e.g., acoustophoresis and optical switching mechanisms. Cell sorting in microfluidics devices are discussed in, e.g., Shields, et al., Microfluidic Cell Sorting: A Review of the Advances in the Separation of Cells from Debulking to Rare Cell Isolation, Lab Chip, 15(5):1230-49 (2015); and U.S. Pub. Nos. 2015/0268244; 2008/0213821; 2020/0190488; and 2005/0164158.

FIG. 2D depicts a method for delivering the gel beads to cells for transfection or transformation. First, cells are provided on a substrate, partitioned into wells or other partitions. Next, gel beads are distributed into the wells or partitions such that there is one gel bead per partition, which can be controlled by the size of the partition and the gel bead. The gel bead is then dissolved or disrupted thereby delivering the contents or “payload” of the gel bead (e.g., the amplified editing cassette constructs and transformation or transfection reagents) to the cells.

The gel beads used in the method depicted in FIG. 2D are dissolvable or degradable upon exposure to one or more stimuli; for example, pH changes, a change in temperature, exposure to light, or exposure to a certain chemical species such as a reducing agent. For example, a degradable gel bead may comprise one or more species with a labile bond such that, when the gel bead is exposed to the appropriate stimuli, the labile bond is broken, and the bead degrades. The labile bond may be a chemical bond or another type of physical interaction such as, e.g., van der Waals interaction, dipole-dipole interaction, or the like. In some cases, the crosslinker used to generate a bead may comprise a labile bond, where, upon exposure to the appropriate conditions, the labile bond can be broken and the gel bead degraded. For example, upon exposure of a polyacrylamide gel bead comprising disulfide crosslinkers to a reducing agent, the disulfide bonds can be broken and the bead degraded. Examples of reducing agents include β-mercaptoethanol, dithiothreitol (DTT), (2S)-2-amino-1,4-dimercaptobutane (dithiobutylamine or DTBA), tris(2-carboxyethyl) phosphine (TCEP), or combinations thereof. Thus, in the method depicted in FIG. 6D, a reducing agent may be delivered to the substrate on which the cells and gel beads have been distributed to dissolve the gel bead.

Cell Growth Modules Rotating Growth Module

As described above, the mammalian cells of choice are initially cultured off-instrument to obtain a suitable number of cells for growth and transfection. The cells are then transferred on instrument to a growth module, three of which are described herein. One growth module is a rotating growth module depicted and described in relation to FIGS. 3A-3E. FIG. 3A shows one embodiment of a rotating growth vial 300 for use with a cell growth module and in the automated multi-module cell processing instruments described herein. The rotating growth vial 300 is an optically-transparent container having an open end 304 for receiving liquid media and cells, a central vial region 306 that defines the primary container for growing cells, a tapered-to-constricted region 318 defining at least one light path 310, a closed end 316, and a drive engagement mechanism 312. The rotating growth vial 300 has a central longitudinal axis 320 around which the vial rotates, and the light path 310 is generally perpendicular to the longitudinal axis of the vial. The first light path 310 is positioned in the lower constricted portion of the tapered-to-constricted region 318. Optionally, some embodiments of the rotating growth vial 300 have a second light path 308 in the tapered region of the tapered-to-constricted region 318. Both light paths in this embodiment are positioned in a region of the rotating growth vial that is constantly filled with the cell culture (cells+growth media) and are not affected by the rotational speed of the growth vial. The first light path 310 is shorter than the second light path 308 allowing for, e.g., sensitive measurement of OD values when the OD values of the cell culture in the vial are at a high level (e.g., later in the cell growth process), whereas the second light path 308 allows for, e.g., sensitive measurement of OD values when the OD values of the cell culture in the vial are at a lower level (e.g., earlier in the cell growth process).

The drive engagement mechanism 312 engages with a motor (not shown) to rotate the vial. In some embodiments, the motor drives the drive engagement mechanism 312 such that the rotating growth vial 300 is rotated in one direction only, and in other embodiments, the rotating growth vial 300 is rotated in a first direction for a first amount of time or periodicity, rotated in a second direction (i.e., the opposite direction) for a second amount of time or periodicity, and this process may be repeated so that the rotating growth vial 300 (and the cell culture contents) are subjected to an oscillating motion. Further, the choice of whether the culture is subjected to oscillation and the periodicity therefor may be selected by the user. The first amount of time and the second amount of time may be the same or may be different. The amount of time may be 1, 2, 3, 4, 5, or more seconds, or may be 1, 2, 3, 4 or more minutes. In another embodiment, in an early stage of cell growth the rotating growth vial 300 may be oscillated at a first periodicity (e.g., every 60 seconds), and then a later stage of cell growth the rotating growth vial 300 may be oscillated at a second periodicity (e.g., every one second) different from the first periodicity.

The rotating growth vial 300 may be reusable or, preferably, the rotating growth vial is consumable. In some embodiments, the rotating growth vial is consumable and is presented to the user pre-filled with growth medium, where the vial is hermetically sealed at the open end 304 with a foil seal. A medium-filled rotating growth vial packaged in such a manner may be part of a kit for use with a stand-alone cell growth device or with a cell growth module that is part of an automated multi-module cell processing system. To introduce cells into the vial, a user need only pipette up a desired volume of cells and use the pipette tip to punch through the foil seal of the vial. Open end 304 may optionally include an extended lip 302 to overlap and engage with the cell growth device. In automated systems, the rotating growth vial 300 may be tagged with a barcode or other identifying means that can be read by a scanner or camera (not shown) that is part of the automated system.

The volume of the rotating growth vial 300 and the volume of the cell culture (including growth medium) may vary, but the volume of the rotating growth vial 300 must be large enough to generate a specified total number of cells. In practice, the volume of the rotating growth vial 300 may range from 5-1000 mL, 10-500 mL, or from 20-250 mL. Likewise, the volume of the cell culture (cells+growth media) should be appropriate to allow proper aeration and mixing in the rotating growth vial 300. Proper aeration promotes uniform cellular respiration within the growth medium. Thus, the volume of the cell culture should be approximately 5-85% of the volume of the growth vial or from 20-60% of the volume of the growth vial. For example, for a 300 mL growth vial, the volume of the cell culture would be from about 15 mL to about 260 mL, or from 6 mL to about 180 mL.

The rotating growth vial 300 preferably is fabricated from a bio-compatible optically transparent material—or at least the portion of the vial comprising a light path for imaging is transparent. Additionally, material from which the rotating growth vial is fabricated should be able to be cooled to about 4° C. or lower and heated to about 55° C. or higher to accommodate both temperature-based cell assays and long-term storage at low temperatures. Further, the material that is used to fabricate the vial must be able to withstand temperatures up to 55° C. without deformation while spinning. Suitable materials include cyclic olefin copolymer (COC), glass, polyvinyl chloride, polyethylene, polyetheretherketone (PEEK), polypropylene, polycarbonate, poly(methyl methacrylate) (PMMA), polysulfone, poly(dimethylsiloxane), and co-polymers of these and other polymers. Preferred materials include polypropylene, polycarbonate, or polystyrene. In some embodiments, the rotating growth vial is inexpensively fabricated by, e.g., injection molding or extrusion.

FIG. 3B illustrates a top view of a rotating growth vial 300. In some examples, the vial 300 may include one or more fins or paddles 322 affixed to an inner surface of the vial wall, where the paddles protrude toward the center of the vial 300. The vial 300 shown in FIG. 3B includes three paddles 322 that are substantially equally spaced around the periphery of the vial 300, but in other examples vial 300 may include two, four, or more paddles 322. The paddles, in some implementations, provide increased mixing and aeration within the vial 300 rotating within a cell growth device, which facilitates cell growth. In other configurations, there may be concentric rows of raised features disposed on the inner surface of the rotating growth vial and the features may be arranged horizontally or vertically; and in other aspects, there may be a spiral configuration of raised features disposed on the inner surface of the rotating growth vial. In alternative aspects, the fins or paddles or concentric rows of raised features may be disposed upon a post or center structure of a rotating growth vial, where the paddles or features radiate out from the center of the vial toward the inner walls of the vial. In some aspects, the width of the paddles or interior features varies with the size or volume of the rotating growth vial, and may range from ⅛ to just under ½ the radius of the rotating growth vial, or from ¼ to ⅓ the radius of the rotating growth vial. The length of the paddles varies with the size or volume of the rotating growth vial and may range from ¼ to ⅘ the length of the rotating growth vial, or from ⅓ to ¾ the length of the rotating growth vial.

In addition, the paddles may be modified to comprise strainers or sieves for dissociating cell aggregates. That is, the paddles may comprise pores that dissociate the cell aggregates, where the pores range in size from 10 to 400 microns in size, or from 20 to 200 microns in size, or from 30 to 100 microns in size. In some embodiments of the automated instruments, there may be two different types of rotating growth vials present, one type without fins and/or strainers or sieves present for cell growth, and one with fins or features and with strainers or sieves for cell dissociation where cells and medium are transferred to and between the growth vial and dissociation vial by an automated liquid handling system.

FIG. 3C is a perspective view of one embodiment of a cell growth device 330. FIG. 3D depicts a cut-away view of the cell growth device 330 from FIG. 3C. In both figures, the rotating growth vial 300 is seen positioned inside a main housing 336 with the extended lip 302 of the rotating growth vial 300 extending above the main housing 336. Additionally, end housings 352, a lower housing 332 and flanges 334 are indicated in both figures. Flanges 334 are used to attach the cell growth device 330 to heating/cooling means or other structure (not shown). FIG. 3D depicts additional detail. In FIG. 3D, upper bearing 342 and lower bearing 340 are shown positioned within main housing 336. Upper bearing 342 and lower bearing 340 support the vertical load of rotating growth vial 300. Lower housing 332 contains the drive motor 338. The cell growth device 330 of FIG. 3C may comprise two light paths; a primary light path 344, and a secondary light path 350. Light path 344 corresponds to light path 310 positioned in the constricted portion of the tapered-to-constricted portion of the rotating growth vial 300, and light path 350 corresponds to light path 308 in the tapered portion of the tapered-to-constricted portion of the rotating growth via 316. Light paths 310 and 308 are not shown in FIG. 3D but may be seen in FIG. 3A. In addition to light paths 344 and 340, there is an emission board 348 to illuminate the light path(s), and detector board 346 to detect the light after the light travels through the cell culture liquid in the rotating growth vial 300.

Cell growth monitoring can be performed by imaging, for example, by allowing the microcarriers to settle and imaging the bottom of the rotating growth vial. Alternatively, an aliquot of the culture is removed and run through a flow cell for imaging. In yet another alternative, the cells may express a fluorescent protein and fluorescence is measured. In yet another alternative, the cell density may be measured by light absorbance at 250-350 nm at light path 310.

The motor 328 engages with drive mechanism 312 and is used to rotate the rotating growth vial 300. In some embodiments, motor 338 is a brushless DC type drive motor with built-in drive controls that can be set to hold a constant revolution per minute (RPM) between 0 and about 3000 RPM. Alternatively, other motor types such as a stepper, servo, brushed DC, and the like can be used. Optionally, the motor 338 may also have direction control to allow reversing of the rotational direction, and a tachometer to sense and report actual RPM. The motor is controlled by a processor (not shown) according to, e.g., standard protocols programmed into the processor and/or user input, and the motor may be configured to vary RPM to cause axial precession of the cell culture thereby enhancing mixing, e.g., to prevent cell aggregation, increase aeration, and optimize cellular respiration.

Main housing 336, end housings 352 and lower housing 332 of the cell growth device 330 may be fabricated from any suitable, robust material including aluminum, stainless steel, or other thermally conductive materials, including plastics. These structures or portions thereof can be created through various techniques, e.g., metal fabrication, injection molding, creation of structural layers that are fused, etc. Whereas the rotating growth vial 300 is envisioned in some embodiments to be reusable, but preferably is consumable, the other components of the cell growth device 330 are preferably reusable and function as a stand-alone benchtop device or as a module in a multi-module cell processing system.

FIG. 3E illustrates a cell growth device 330 as part of an assembly comprising the cell growth device 330 of FIG. 3C coupled to light source 390, detector 392, and thermal components 394. The rotating growth vial 300 is inserted into the cell growth device. Components of the light source 390 and detector 392 (e.g., such as a photodiode with gain control to cover 5-log) are coupled to the main housing of the cell growth device. The lower housing 332 that houses the motor that rotates the rotating growth vial 300 is illustrated, as is one of the flanges 334 that secures the cell growth device 330 to the assembly. Also, the thermal components 394 illustrated are a Peltier device or thermoelectric cooler. In this embodiment, thermal control is accomplished by attachment and electrical integration of the cell growth device 330 to the thermal components 394 via the flange 334 on the base of the lower housing 332. Thermoelectric coolers are capable of “pumping” heat to either side of a junction, either cooling a surface or heating a surface depending on the direction of current flow. In one embodiment, a thermistor is used to measure the temperature of the main housing and then, through a standard electronic proportional-integral-derivative (PID) controller loop, the rotating growth vial 300 is controlled to approximately +/−0.5° C. In yet another alternative, the detector is replaced with an imaging camera. The geometry of the constricted portion of the rotating growth vial 300 containing light path 310 is further tapered to collect settled cell aggregates or microcarriers coated with cells when rotation is paused. The stacked cell aggregates or microcarriers with cells are imaged. Total cell number can be derived from the height of the stacked cell aggregates. Total cell number can be derived from the combined height of the microcarriers coated with cells and the observed confluency of cells on a subset of microcarriers.

In use, cells are inoculated (cells can be pipetted, e.g., from an automated liquid handling system or by a user) into pre-filled growth media of a rotating growth vial 300 by piercing though the foil seal or film. The programmed software of the cell growth device 330 sets the control temperature for growth, typically 30° C., then slowly starts the rotation of the rotating growth vial 300. The cell/growth media mixture slowly moves vertically up the wall due to centrifugal force allowing the rotating growth vial 300 to expose a large surface area of the mixture to an O₂ or CO₂ environment. If enhanced mixing is required, e.g., to optimize growth conditions, the speed of the vial rotation can be varied to cause an axial precession of the liquid, and/or a complete directional change can be performed at programmed intervals.

In addition to imaging, other cell growth parameters can be measured. Other optional measures of cell growth may be made including spectroscopy using visible, UV, or near infrared (NIR) light, measuring, e.g., the concentration of nutrients and/or wastes in the cell culture and/or other spectral properties can be measured via, e.g., dielectric impedance spectroscopy, visible fluorescence, fluorescence polarization, or luminescence. Additionally, the cell growth device 330 may include additional sensors for measuring, e.g., dissolved oxygen, carbon dioxide, pH, conductivity, and the like. For additional details regarding rotating growth vials and cell growth devices see U.S. Pat. Nos. 10,435,662; and 10,443,031; and U.S. Ser. No. 16/552,981, filed 7 Aug. 2019; and Ser. No. 16/780,640, filed 3 Feb. 2020.

Tangential Flow Filtration Module

An alternative to the rotating growth module for growing cells off-instrument or as a growth module for an automated instrument is a tangential flow filtration (TFF) module as shown in FIGS. 4A-4G. The TFF module shown in FIGS. 4A-4G is a module that can grow, perform buffer exchange, concentrate cells and dissociate cells so that the cells may be transfected or transduced with the nucleic acids needed for engineering or editing the cell's genome.

FIG. 4A shows a retentate member 422 (top), permeate member 420 (middle) and a tangential flow assembly 410 (bottom) comprising the retentate member 422, membrane 424 (not seen in FIG. 4A), and permeate member 420 (also not seen). In FIG. 4A, retentate member 422 comprises a tangential flow channel 402, which has a serpentine configuration that initiates at one lower corner of retentate member 422—specifically at retentate port 428—traverses across and up then down and across retentate member 422, ending in the other lower corner of retentate member 422 at a second retentate port 428. Also seen on retentate member 422 are energy directors 491, which circumscribe the region where a membrane or filter (not seen in this FIG. 4A) is seated, as well as interdigitate between areas of channel 402. Energy directors 491 in this embodiment mate with and serve to facilitate ultrasonic welding or bonding of retentate member 422 with permeate/filtrate member 420 via the energy director component 491 on permeate/filtrate member 420 (at right). Additionally, countersinks 423 can be seen, two on the bottom one at the top middle of retentate member 422. Countersinks 423 are used to couple and tangential flow assembly 410 to a reservoir assembly (not seen in this FIG. 4A but see FIG. 4B).

Permeate/filtrate member 420 is seen in the middle of FIG. 4A and comprises, in addition to energy director 491, through-holes for retentate ports 428 at each bottom corner (which mate with the through-holes for retentate ports 428 at the bottom corners of retentate member 422), as well as a tangential flow channel 402 and two permeate/filtrate ports 426 positioned at the top and center of permeate member 420. The tangential flow channel 402 structure in this embodiment has a serpentine configuration and an undulating geometry, although other geometries may be used. Permeate member 420 also comprises countersinks 423, coincident with the countersinks 423 on retentate member 420.

At bottom is a tangential flow assembly 410 comprising the retentate member 422 and permeate member 420 seen in this FIG. 4A. In this view, retentate member 422 is “on top” of the view, a membrane (not seen in this view of the assembly) would be adjacent and under retentate member 422 and permeate member 420 (also not seen in this view of the assembly) is adjacent to and beneath the membrane. Again countersinks 423 are seen, where the countersinks in the retentate member 422 and the permeate member 420 are coincident and configured to mate with threads or mating elements for the countersinks disposed on a reservoir assembly (not seen in FIG. 4A but see FIG. 4B).

A membrane or filter is disposed between the retentate and permeate members, where fluids can flow through the membrane but cells cannot and are thus retained in the flow channel disposed in the retentate member. Filters or membranes appropriate for use in the TFF device/module are those that are solvent resistant, are contamination free during filtration, and are able to retain the types and sizes of cells of interest. For example, in order to retain small cell types, pore sizes can be as low as 0.5 μm, however for other cell types, the pore sizes can be as high as 20 μm. Indeed, the pore sizes useful in the TFF device/module include filters with sizes from 0.50 μm and larger. The filters may be fabricated from any suitable non-reactive material including cellulose mixed ester (cellulose nitrate and acetate) (CME), polycarbonate (PC), polyvinylidene fluoride (PVDF), polyethersulfone (PES), polytetrafluoroethylene (PTFE), nylon, glass fiber, or metal substrates as in the case of laser or electrochemical etching.

The length of the channel structure 402 may vary depending on the volume of the cell culture to be grown. The length of the channel structure typically is from 60 mm to 300 mm, or from 70 mm to 200 mm, or from 80 mm to 100 mm. The cross-section configuration of the flow channel 402 may be round, elliptical, oval, square, rectangular, trapezoidal, or irregular. If square, rectangular, or another shape with generally straight sides, the cross section may be from about 10 μm to 1000 μm wide, or from 200 μm to 800 μm wide, or from 300 μm to 700 μm wide, or from 400 μm to 600 μm wide; and from about 10 μm to 1000 μm high, or from 200 μm to 800 μm high, or from 300 μm to 700 μm high, or from 400 μm to 600 μm high. If the cross section of the flow channel 302 is generally round, oval or elliptical, the radius of the channel may be from about 50 μm to 1000 μm in hydraulic radius, or from 5 μm to 800 μm in hydraulic radius, or from 200 μm to 700 μm in hydraulic radius, or from 300 μm to 600 μm wide in hydraulic radius, or from about 200 to 500 μm in hydraulic radius. Moreover, the volume of the channel in the retentate 422 and permeate 420 members may be different depending on the depth of the channel in each member.

FIG. 4B shows front perspective (right) and rear perspective (left) views of a reservoir assembly 450 configured to be used with the tangential flow assembly 410 seen in FIG. 4A. Seen in the front perspective view (e.g., “front” being the side of reservoir assembly 450 that is coupled to the tangential flow assembly 410 seen in FIG. 4A) are retentate reservoirs 452 on either side of permeate reservoir 454. Also seen are permeate ports 426, retentate ports 428, and three threads or mating elements 425 for countersinks 423 (countersinks 423 not seen in this FIG. 4B). Threads or mating elements 425 for countersinks 423 are configured to mate or couple the tangential flow assembly 410 (seen in FIG. 4A) to reservoir assembly 450. Alternatively, or in addition, fasteners, sonic welding or heat stakes may be used to mate or couple the tangential flow assembly 410 to reservoir assembly 450. In addition is seen gasket 445 covering the top of reservoir assembly 450. Gasket 445 is described in detail in relation to FIG. 4E. At left in FIG. 4B is a rear perspective view of reservoir assembly 450, where “rear” is the side of reservoir assembly 450 that is not coupled to the tangential flow assembly. Seen are retentate reservoirs 452, permeate reservoir 454, and gasket 445.

The TFF device may be fabricated from any robust material in which channels (and channel branches) may be milled including stainless steel, silicon, glass, aluminum, or plastics including cyclic-olefin copolymer (COC), cyclo-olefin polymer (COP), polystyrene, polyvinyl chloride, polyethylene, polyethylene, polypropylene, acrylonitrile butadiene, polycarbonate, polyetheretheketone (PEEK), poly(methyl methylacrylate) (PMMA), polysulfone, and polyurethane, and co-polymers of these and other polymers. If the TFF device/module is disposable, preferably it is made of plastic. In some embodiments, the material used to fabricate the TFF device/module is thermally-conductive so that the cell culture may be heated or cooled to a desired temperature. In certain embodiments, the TFF device is formed by precision mechanical machining, laser machining, electro discharge machining (for metal devices); wet or dry etching (for silicon devices); dry or wet etching, powder or sandblasting, photostructuring (for glass devices); or thermoforming, injection molding, hot embossing, or laser machining (for plastic devices) using the materials mentioned above that are amenable to this mass production techniques.

FIG. 4C depicts a top-down view of the reservoir assemblies 450 shown in FIG. 4B. FIG. 4D depicts a cover 444 for reservoir assembly 450 shown in FIGS. 4B and 4E depicts a gasket 445 that in operation is disposed on cover 444 of reservoir assemblies 450 shown in FIG. 4B. FIG. 4C is a top-down view of reservoir assembly 450, showing the tops of the two retentate reservoirs 452, one on either side of permeate reservoir 454. Also seen are grooves 432 that will mate with a pneumatic port (not shown), and fluid channels 434 that reside at the bottom of retentate reservoirs 452, which fluidically couple the retentate reservoirs 452 with the retentate ports 428 (not shown), via the through-holes for the retentate ports in permeate member 420 and membrane 424 (also not shown). FIG. 4D depicts a cover 444 that is configured to be disposed upon the top of reservoir assembly 450. Cover 444 has round cut-outs at the top of retentate reservoirs 452 and permeate/filtrate reservoir 454. Again, at the bottom of retentate reservoirs 452 fluid channels 434 can be seen, where fluid channels 434 fluidically couple retentate reservoirs 452 with the retentate ports 428 (not shown). Also shown are three pneumatic ports 430 for each retentate reservoir 452 and permeate/filtrate reservoir 454. FIG. 4E depicts a gasket 445 that is configures to be disposed upon the cover 444 of reservoir assembly 450. Seen are three fluid transfer ports 442 for each retentate reservoir 452 and for permeate/filtrate reservoir 454. Again, three pneumatic ports 330, for each retentate reservoir 452 and for permeate/filtrate reservoir 454, are shown.

The overall work flow for cell growth comprises loading a cell culture to be grown into a first retentate reservoir, preferably bubbling air or an appropriate gas through the cell culture, passing or flowing the cell culture through the first retentate port then tangentially through the TFF channel structure while collecting medium or buffer through one or both of the permeate ports 426, collecting the cell culture through a second retentate port 428 into a second retentate reservoir, optionally adding additional fresh or different medium to the cell culture and optionally bubbling air or gas through the cell culture, then repeating the process, all while measuring, e.g., the optical density of the cell culture in the retentate reservoirs continuously or at desired intervals. Again, cell growth monitoring can be performed by imaging, for example, by allowing the microcarriers to settle and imaging the bottom of the TFF retentate reservoir. Alternatively, an aliquot of the culture is removed and run through a flow cell for imaging. In yet another alternative, the cells may express a fluorescent protein and fluorescence is measured.

In the channel structure, the membrane bifurcating the flow channels retains the cells on one side of the membrane (the retentate side 422) and allows unwanted medium or buffer to flow across the membrane into a filtrate or permeate side (e.g., permeate member 420) of the device. Bubbling air or other appropriate gas through the cell culture both aerates and mixes the culture to enhance cell growth. During the process, medium that is removed during the flow through the channel structure is removed through the permeate/filtrate ports 426. Alternatively, cells can be grown in one reservoir with bubbling or agitation without passing the cells through the TFF channel from one reservoir to the other.

The overall work flow for cell concentration using the TFF device/module involves flowing a cell culture or cell sample tangentially through the channel structure. As with the cell growth process, the membrane bifurcating the flow channels retains the cells on one side of the membrane and allows unwanted medium or buffer to flow across the membrane into a permeate/filtrate side (e.g., permeate member 420) of the device. In this process, a fixed volume of cells in medium or buffer is driven through the device until the cell sample is collected into one of the retentate ports 428, and the medium/buffer that has passed through the membrane is collected through one or both of the permeate/filtrate ports 426. All types of prokaryotic and eukaryotic cells—both adherent and non-adherent cells—can be grown in the TFF device. Adherent cells may be grown on beads or other cell scaffolds suspended in medium that flow through the TFF device.

The medium or buffer used to suspend the cells in the cell concentration device/module may be any suitable medium or buffer for the type of cells being transformed or transfected, such as MEM, DMEM, IMDM, RPMI, Hanks', PBS and Ringer's solution, where the media may be provided in a reagent cartridge as part of a kit. For culture of adherent cells, cells may be disposed on microcarriers or other type of scaffold suspended in medium. The microcarriers of particular use typically have a diameter of 50-500 μm and have a density slightly greater than that of the culture medium thus facilitating an easy separation of cells and medium for, e.g., medium exchange yet the density must also be sufficiently low to allow complete suspension of the carriers at a minimum stirring rate in order to avoid hydrodynamic damage to the cells.

In both the cell growth and concentration processes, passing the cell sample through the TFF device and collecting the cells in one of the retentate ports 428 while collecting the medium in one of the permeate/filtrate ports 426 is considered “one pass” of the cell sample. The transfer between retentate reservoirs “flips” the culture. The retentate and permeate ports collecting the cells and medium, respectively, for a given pass reside on the same end of TFF device/module with fluidic connections arranged so that there are two distinct flow layers for the retentate and permeate/filtrate sides, but if the retentate port 428 resides on the retentate member of device/module (that is, the cells are driven through the channel above the membrane and the filtrate (medium) passes to the portion of the channel below the membrane), the permeate/filtrate port 426 will reside on the permeate member of device/module and vice versa (that is, if the cell sample is driven through the channel below the membrane, the filtrate (medium) passes to the portion of the channel above the membrane). Due to the high pressures used to transfer the cell culture and fluids through the flow channel of the TFF device, the effect of gravity is negligible.

At the conclusion of a “pass” in either of the growth and concentration processes, the cell sample is collected by passing through the retentate port 428 and into the retentate reservoir (not shown). To initiate another “pass”, the cell sample is passed again through the TFF device, this time in a flow direction that is reversed from the first pass. The cell sample is collected by passing through the retentate port 428 and into retentate reservoir (not shown) on the opposite end of the device/module from the retentate port 428 that was used to collect cells during the first pass. Likewise, the medium/buffer that passes through the membrane on the second pass is collected through the permeate port 426 on the opposite end of the device/module from the permeate port 426 that was used to collect the filtrate during the first pass, or through both ports. This alternating process of passing the retentate (the concentrated cell sample) through the device/module is repeated until the cells have been grown to a desired optical density, and/or concentrated to a desired volume, and both permeate ports (i.e., if there are more than one) can be open during the passes to reduce operating time. In addition, buffer exchange may be effected by adding a desired buffer (or fresh medium) to the cell sample in the retentate reservoir, before initiating another “pass”, and repeating this process until the old medium or buffer is diluted and filtered out and the cells reside in fresh medium or buffer. Note that buffer exchange and cell growth may (and typically do) take place simultaneously, and buffer exchange and cell concentration may (and typically do) take place simultaneously. For further information and alternative embodiments on TFFs see, e.g., U.S. Ser. No. 16/798,302, filed 22 Feb. 2020.

In addition, the TFF may be modified to dissociate cells, as shown in FIGS. 4F and 4G. That is, the TFF may be modified such that the retentate reservoirs, in addition to being connected through the flow channel that courses through the TFF device, are connected directly by a conduit where the cells are passed from one retentate reservoir to another without being sent through the flow channel. In FIG. 4F, retentate reservoirs 452 are shown, connected by conduit 462. In conduit 462 are placed one to many (e.g., in FIG. 4G, there are three) strainers, frits or sieves 460 through which aggregates of cells are passed to dissociate the aggregates. As with the modified paddles or features in the rotating growth vial, strainers, frits or sieves 460 comprise pores or openings from 10 to 400 microns in size, or from 20 to 200 microns in size, or from 30 to 100 microns in size configured to dissociate the cell aggregates. That is, the TFF may be used to grow the cells—either as aggregates or on microcarriers—passage the cells to increase the number of cells, concentrate the cells and then finally the cells may be routed through the direct conduit between the retentate reservoirs to dissociate the cells for transfection/transduction.

Bioreactor

In addition to the rotating growth vial module shown in FIGS. 3A-3E and described in the related text, and the tangential flow filtration module shown FIG. 4A-4G and described in the related text, a bioreactor can be used to grow cells off-instrument or to allow for cell growth and recovery on-instrument; e.g., as one module of the multi-module automated instrument. Additionally, the bioreactor can be used to generate emulsions using the impeller and oil for encapsulated delivery of editing reagents, e.g., by encapsulating cells and small reagent delivery vehicles in dissolvable gel beads, or by encapsulating cells and larger non-dissolvable reagent delivery vehicles to form uniform droplets with a thin aqueous layer. The bioreactor may also be used to break emulsions either those formed in the bioreactor itself or those formed on a microfluidic device and transferred to the bioreactor—using, e.g., the action of the impeller and a breaking agent such as perfluoro-1-octanol. Further, the bioreactor supports cell selection/enrichment, via expressed antibiotic markers in the growth process or via expressed antibodies coupled to magnetic beads and a magnet associated with the bioreactor. There are many bioreactors known in the art, including those described in, e.g., WO 2019/046766; 10,699,519; 10,633,625; 10,577,576; 10,294,447; 10,240,117; 10,179,898; 10,370,629; and 9,175,259; and those available from Lonza Group Ltd. (Basel, Switzerland); Miltenyi Biotec (Bergisch Gladbach, Germany), Terumo BCT (Lakewood, Colo.) and Sartorius GmbH (Gottingen, Germany).

FIG. 5A shows one embodiment of a bioreactor assembly 500 for cell growth in the automated multi-module cell processing instruments described herein. Unlike most bioreactors that are used to support fermentation or other processes with an eye to harvesting the products produced by organisms grown in the bioreactor, the present bioreactor (and the processes performed therein) is configured to grow cells, monitor cell growth (e.g., via optical means and/or capacitance), passage cells, transfect or transduce cells, select and/or enrich cells, and support editing, expansion and harvesting of edited cells. Bioreactor assembly 500 comprises a growth vessel 501 comprising tapered a main body 504 with a lid assembly 502 comprising ports 508, including an optional motor integration port 510 driving impeller 506 via impeller shaft 552. The tapered shape of main body 504 of the vessel 501 along with, in some embodiments, dual impellers allows for working with a larger dynamic range of volumes, such as, e.g., up to 500 ml and as low as 100 ml for rapid sedimentation of the microcarriers. In addition, the low volume is useful for magnetic bead separation or enrichment as described above.

Bioreactor assembly 500 further comprises bioreactor stand assembly 503 comprising a main body 512 and vessel holder 514 comprising a heat jacket or other heating means (not shown, but see FIG. 5E) into which the main body 504 of vessel 501 is disposed in operation. The main body 504 of vessel 501 is biocompatible and preferably transparent—in some embodiments, in the UV and IR range as well as the visible spectrum—so that the growing cells can be visualized by, e.g., cameras or sensors integrated into lid assembly 502 or through viewing apertures or slots in the main body 512 of bioreactor stand assembly 503 (not shown in this FIG. 5A, but see FIG. 5E).

Bioreactor assembly 500 supports growth of cells from a 500,000 cell input to a 10 billion cell output, or from a 1 million cell input to a 25 billion cell output, or from a 5 million cell input to a 50 billion cell output or combinations of these ranges depending on, e.g., the size of main body 504 of vessel 501, the medium used to grow the cells, whether the cells are adherent or non-adherent. The bioreactor that comprises assembly 500 supports growth of both adherent and non-adherent cells, wherein adherent cells are typically grown of microcarriers as described in detail above and supra or as spheroids. Alternatively, another option for growing mammalian cells in the bioreactor described herein is growing single cells in suspension using a specialized medium such as that developed by ACCELLTA™ (Haifa, Israel). As described above, cells grown in this medium must be adapted to this process over many cell passages; however, once adapted the cells can be grown to a density of >40 million cells/ml and expanded 50-100× in approximately a week, depending on cell type.

Main body 504 of vessel 501 preferably is manufactured by injection molding, as is, in some embodiments, impeller 506 and the impeller shaft (not shown). Impeller 506 also may be fabricated from stainless steel, metal, plastics or the polymers listed infra. Injection molding allows for flexibility in size and configuration and also allows for, e.g., volume markings to be added to the main body 504 of vessel 501. Additionally, material from which the main body 504 of vessel 501 is fabricated should be able to be cooled to about 4° C. or lower and heated to about 55° C. or higher to accommodate cell growth. Further, the material that is used to fabricate the vial preferably is able to withstand temperatures up to 55° C. without deformation. Suitable materials for main body 504 of vessel 501 include those described for the rotating growth vial described in relation to FIGS. 3A and 3B and the TFF device described in relation to FIG. 4A-4E, including cyclic olefin copolymer (COC), glass, polyvinyl chloride, polyethylene, polyetheretherketone (PEEK), polypropylene, polycarbonate, poly(methyl methacrylate) (PMMA), polysulfone, poly(dimethylsiloxane), cyclo-olefin polymer (COP), and co-polymers of these and other polymers. Preferred materials include polypropylene, polycarbonate, or polystyrene. The material used for fabrication may depend on the cell type to be grown, and is conducive to growth of both adherent and non-adherent cells. The main body 504 of vessel 501 may be reusable or, alternatively, may be manufactured and configured for a single use. In one embodiment, main body 504 of vessel 501 may support cell culture volumes of 25 ml to 500 ml, but may be scaled up to support cell culture volumes of up to 3 L.

The bioreactor stand assembly comprises a stand or frame 550, a main body 512 which holds the vessel 501 during operation. The stand/frame 550 and main body 512 are fabricated from stainless steel, other metals, or polymer/plastics. The bioreactor main body further comprises a heat jacket (not seen in FIG. 5A, but see FIG. 5E) to maintain the bioreactor main body 504—and thus the cell culture—at a desired temperature. Essentially, the stand assembly can host a set of sensors and cameras to monitor cell culture.

FIG. 5B depicts a top-down view of one embodiment of vessel lid assembly 502. Vessel lid assembly 502 is configured to be air-tight, providing a sealed, sterile environment for cell growth as well as to provide biosafety thus maintaining a closed system. Vessel lid assembly 502 and the main body 504 of vessel 501 can be sealed via fasteners such as screws, using biocompatible glues, or the two components may be ultrasonically welded. Vessel lid assembly 502 is some embodiments is fabricated from stainless steel such as S316L stainless steel but may also be fabricated from metals, other polymers (such as those listed supra) or plastics. As seen in this FIG. 5B—as well as in FIG. 5A—vessel lid assembly 502 comprises a number of different ports to accommodate liquid addition and removal; gas addition and removal; for insertion of sensors to monitor culture parameters (described in more detail infra); to accommodate one or more cameras or other optical sensors; to provide access to the main body 504 of vessel 501 by, e.g., a liquid handling device; and to accommodate a motor for motor integration to drive one or more impellers 506. Exemplary ports depicted in FIG. 5B include three liquid-in ports 516 (at 4 o'clock, 6 o'clock and 8 o'clock), one liquid-out port 522 (at 11 'clock), a capacitance sensor 518 (at 9 o'clock), one “gas in” port 524 (at 12 o'clock), one “gas out” port 520 (at 10 o'clock), an optical sensor 526 (at 1 o'clock), a rupture disc 528 at 2 o'clock, a self-sealing port 530 (at 3 o'clock) to provide access to the main body 504 of growth vessel 501; and (a temperature probe 532 (at 5 o'clock).

The ports 508 shown in vessel lid assembly 502 in this FIG. 5B are exemplary only and it should be apparent to one of ordinary skill in the art given the present disclosure that, e.g., a single liquid-in port 516 could be used to accommodate addition of all liquids to the cell culture rather than having a liquid-in port for each different liquid added to the cell culture. Similarly, there may be more than one gas-in port 524, such as one for each gas, e.g., O₂, CO₂ that may be added. In addition, although a temperature probe 532 is shown, a temperature probe alternatively may be located on the outside of vessel holder 514 of bioreactor stand assembly 503 separate from or integrated into heater jacket 548 (not seen in this FIG. 5B, but see FIG. 5E). A self-sealing port 530, if present, allows access to the main body 504 of vessel 501 for, e.g., a pipette, syringe, or other liquid delivery system via a gantry (not shown). As shown in FIG. 5A, additionally there may be a motor integration port to drive the impeller(s), although in other configurations of vessel 501 may alternatively integrate the motor drive at the bottom of the main body 504 of vessel 501. Vessel lid assembly 502 may also comprise a camera port for viewing and monitoring the cells.

Additional sensors include those that detect O₂ concentration, a CO₂ concentration, culture pH, lactate concentration, glucose concentration, biomass, and optical density. The sensors may use optical (e.g., fluorescence detection), electrochemical, or capacitance sensing and either be reusable or configured and fabricated for single-use. Sensors appropriate for use in the bioreactor are available from Omega Engineering (Norwalk Conn.); PreSens Precision Sensing (Regensburg, Germany); C-CIT Sensors AG (Waedenswil, Switzerland), and ABER Instruments Ltd. (Alexandria, Va.). In one embodiment, optical density is measured using a reflective optical density sensor to facilitate sterilization, improve dynamic range and simplify mechanical assembly. The rupture disc, if present, provides safety in a pressurized environment, and is programmed to rupture if a threshold pressure is exceeded in the bioreactor. If the cell culture in the bioreactor vessel is a culture of adherent cells, microcarriers may be used as described supra. In such an instance, the liquid-out port may comprise a filter such as a stainless steel or plastic (e.g., polyvinylidene difluoride (PVDF), nylon, polypropylene, polybutylene, acetal, polyethylene, or polyamide) filter or frit to prevent microcarriers from being drawn out of the culture during, e.g., medium exchange, but to allow dead cells to be withdrawn from the vessel. The microcarriers used for initial cell growth can be nanoporous (where pore sizes are typically <20 nm in size), microporous (with pores between >20 nm to <1 μm in size), or macroporous (with pores between >1 μm in size, e.g., 20 μm) and the microcarriers are typically 50-200 μm in diameter; thus the pore size of the filter or frit in the liquid-out port will differ depending on microcarrier size.

The microcarriers used for cell growth depend on cell type and desired cell numbers, and typically include a coating of a natural or synthetic extracellular matrix or cell adhesion promoters (e.g., antibodies to cell surface proteins or poly-L-lysine) to promote cell growth and adherence. Microcarriers for cell culture are widely commercially available from, e.g., Millipore Sigma, (St. Louis, Mo., USA); ThermoFisher Scientific (Waltham, Mass., USA); Pall Corp. (Port Washington, N.Y., USA); GE Life Sciences (Marlborough, Mass., USA); and Corning Life Sciences (Tewkesbury, Mass., USA). As for the extracellular matrix, natural matrices include collagen, fibrin and vitronectin (available, e.g., from ESBio, Alameda, Calif., USA), and synthetic matrices include MATRIGEL® (Corning Life Sciences, Tewkesbury, Mass., USA), GELTREX™ (ThermoFisher Scientific, Waltham, Mass., USA), CULTREX® (Trevigen, Gaithersburg, Md., USA), biomemetic hydrogels available from Cellendes (Tubingen, Germany); and tissue-specific extracellular matrices available from Xylyx (Brooklyn, N.Y., USA); further, denovoMatrix (Dresden, Germany) offers screenMATRIX™, a tool that facilitates rapid testing of a large variety of cell microenvironments (e.g., extracellular matrices) for optimizing growth of the cells of interest.

FIG. 5C is a side view of the main body 504 of vessel 501. A portion of vessel lid assembly 502 can be seen, as well as two impellers 506 a and 506 b. Also seen are a lactate/glucose sensor probe 534, a pH, O₂, CO₂ sensor 536 (such as a PRESENS™ integrated optical sensor (Precision Sensing GmbH, (Regensburg, Germany)), and a viable biomass sensor 538 (such as, e.g., the FUTURA PICO™ capacitance sensor (ABER, Alexandria Va.)). In some embodiments, flat regions are fabricated onto the main body 504 of vessel 501 to reduce optical loss, simplify spot placement and simplify fluorescent measurement of pH, dO₂, and dCO₂.

FIG. 5D shows exemplary design guidelines for a one-impeller embodiment (left) and a two-impeller embodiment (right) of the main body 504 of vessel 501, including four exemplary impeller configurations. The embodiment of the INSCRIPTA™ bioreactor vessel 501 main body 504 as shown in this FIG. 5D has a total volume of 820 ml and supports culture volumes from 25 ml to 500 ml. As mentioned above, the impellers (and impeller shaft) may be injection molded or may be fabricated from stainless steel, other biocompatible metals, polymers or plastics and preferably comprised polished surfaces to facilitate sterilization. The impeller may be configured as a turbine-, pitched-blade-, hydrofoil- or marine-type impeller. In a two-impeller configuration, the impellers may be of the same type or different types. In the bioreactors described herein (the “INSCRIPTA™ bioreactors”) and used to generated the data in Examples IV-XI, agitation is provided at 0-100 rpm, or 40-80 rpm, or approximately 70 rpm during cell growth (depending on the cell type being cultured); however, lower or higher revolutions per minute may be used depending on the volume of the main body 504 of vessel 501, the type of cells being cultured, whether the cells are adherent and being grown on microcarriers or the cells are non-adherent, and the size and configuration of the impellers. The impeller may turn in a clockwise direction, a counter-clockwise direction or the impeller may change direction (oscillate) or stop at desired intervals, particularly during cell detachment from the microcarriers. Also, intermittent agitation may be applied, e.g., agitating for 10 minutes every 30 minutes, or agitating for 1 minute every 5 minutes or any other desired pattern. Additionally, impeller rpm is often increased (e.g., up to 4000 rpm) when the cells are being detached from microcarriers. Although the present embodiment of INSCRIPTA™ bioreactor utilizes one or more impellers for cell growth, alternative embodiments of the INSCRIPTA™ bioreactor described herein may utilize bubbling or other physical mixing means.

Also seen in FIG. 5D is an equation that gives a range for exemplary bioreactor dimensions base on the height (H) and thickness (T) of the main body of vessel 504. For example, D=0.25−05*T means the impeller diameter could be one quarter or one half of the main body of vessel 504 thickness, T. C is the clearance of the impeller from the bottom of the main body of vessel 504, which can be 0.15 to 0.5 times the thickness. It should be apparent to one of ordinary skill in the art given the present disclosure that these numbers are just one embodiment and the ranges may be larger. The bioreactor vessel 501 main body 504 comprises an 8-10 mm clearance from the bottom of the main body 504 of vessel 501 to the lower impeller 506 b and the lower impeller 506 b and the upper impeller 506 a are approximately 40 mm apart.

FIG. 5E is a side view of the vessel holder portion 514 of the bioreactor stand main body 512 of the bioreactor stand assembly 503. Inner surface 540 of vessel holder 514 is indicated and shown are camera or fiber optic ports 546 for monitoring, e.g., cell growth and viability; O₂ and CO₂ levels, and pH. The vessel holder portion 514 of the bioreactor stand main body 512 may also provide illumination using LED lights, such as a ring of LED lights (not shown). FIG. 5F is a side perspective view of the assembled bioreactor without sensors 542. Seen are vessel lid assembly 502, bioreactor stand assembly 503, bioreactor stand main body 512 into which the main body 504 of vessel 501 (not seen in FIG. 5E) is inserted. FIG. 5G is a lower side perspective view of bioreactor assembly 500 showing bioreactor stand assembly 503, bioreactor stand main body 512, vessel lid assembly 502 and two camera mounts 544. Surrounding bioreactor stand main body 512 is heater jacket 548.

FIG. 5H is an exemplary diagram of the bioreactor fluidics. Fluidics and pneumatics are designed to establish a cell culture environment conducive for mammalian cell growth, including iPSCs. Fluidic circuits are designed to deliver and/or remove cell medium, buffers, microcarriers and additional reagents needed for growth, maintenance, selection and passaging of the cells in the automated closed culture instrument. The pneumatic circuits are designed to deliver the appropriate gas mixture and humidity for the chosen cell type, and may comprise line-in filters to prevent any contaminants from reaching the bioreactor.

FIG. 5I is a block diagram for an exemplary bioreactor control system. The control system is designed to control and automate the fluidics, pneumatics and sensor function in a closed system and without human intervention. In one embodiment, the control system is based on state-machines with a user editable state order and parameters using Json and jsonette config files. State-machines allow for dynamic control of several aspects of the bioreactor with a single computer.

In use, the bioreactor described herein is used for cell growth and expansion—either before or after the cells are transfected in droplets—as well as for medium exchange and cell concentration. Also mentioned supra, the bioreactor may be used to generate emulsions/droplets using the impeller and added oil, e.g., by encapsulating cells and small reagent delivery vehicles in dissolvable gel beads, or by encapsulating cells and larger non-dissolvable reagent delivery vehicles to form uniform droplets with a thin aqueous layer. The bioreactor may also be used to break emulsions—either those formed in the bioreactor itself or those formed on a microfluidic device and transferred to the bioreactor—using, e.g., the action of the impeller and a breaking agent such as perfluoro-1-octanol.

Medium/buffer exchange is in one embodiment accomplished using gravitational sedimentation and aspiration via a filter in the liquid-out port where the filter is of an appropriate size to retain microcarriers (see, e.g., Example VII, infra). In one embodiment used with the present bioreactor, a frit with pore size 100 μm was used and microcarriers with diameters or 120-225 μm were used in the cell culture. Sedimentation was accomplished in approximately 2-3 minutes for a 100 ml culture and 4-5 minutes for a 500 ml culture. The medium was aspirated at >100 ml/min rate. In addition to clearing the medium from the main body 504 of vessel 501, dead cells were removed as well. If sedimentation is used, the microcarriers do not typically accumulate on the filter; however, if accumulation is detected, the medium in the liquid-out port can be pushed back into main body 504 of vessel 501 in a pulse. In some embodiments—particularly those where sedimentation is not used—a cycle of aspiration, release (push back), aspiration and release (push back) may be performed. Experimental results show that medium exchange (aspiration) at ˜200 ml/min does not impact cell growth (see FIG. 14).

Exemplary Solid Wall Module for Delivering Reagent Bundle Droplets to Cells

Returning to the solid wall delivery embodiment, FIGS. 6A-6D depict a solid wall device 650 for partitioning mammalian cells in microwells in a solid wall isolation, incubation, and normalization (SWIIN) module. FIG. 6A depicts an embodiment of a SWIIN module 650 from an exploded top perspective view. In SWIIN module 650 the retentate member is formed on the bottom of a top of a SWIIN module component and the permeate member is formed on the top of the bottom of a SWIIN module component.

The SWIIN module 650 in FIG. 6A comprises from the top down, a reservoir gasket or cover 658, a retentate member 604 (where a retentate flow channel cannot be seen in this FIG. 6A), a perforated member 601 swaged with a filter (filter not seen in FIG. 6A), a permeate member 608 comprising integrated reservoirs (permeate reservoirs 652 and retentate reservoirs 654, one of each seen in this perspective view), and two reservoir seals 662, which seal the bottom of permeate reservoirs 652 and retentate reservoirs 654. A permeate channel 660 a can be seen disposed on the top of permeate member 608, defined by a raised portion 676 of serpentine channel 660 a, and ultrasonic tabs 664 can be seen disposed on the top of permeate member 608 as well. The perforations that form the wells on perforated member 601 are not seen in this FIG. 6A; however, through-holes 666 to accommodate the ultrasonic tabs 664 are seen. In addition, supports 670 are disposed at either end of SWIIN module 650 to support SWIIN module 650 and to elevate permeate member 608 and retentate member 604 above reservoirs 652 and 654 to minimize bubbles or air entering the fluid path from the permeate reservoir to serpentine channel 660 a or the fluid path from the retentate reservoir to serpentine channel 660 b (neither fluid path is seen in this FIG. 6A). In yet another alternative, the filter is bonded to perforated member 601 using an adhesive. In yet another alternative, the filter bottom of each well is patterned with two electrodes to perform electroporation. These electrodes may be patterned in an interdigitated format with one electrode being the anode and the other electrode being the cathode. In yet another alternative, one electrode is in the permeate chamber and the other electrode is in the retentate chamber. In an alternative approach, reagents for delivery are printed on the filter in the wells during the manufacturing process. Printing reagents on the filter could be performed before or after swaging or bonding filter membrane to the perforated metal.

In this FIG. 6A, it can be seen that the serpentine channel 660 a that is disposed on the top of permeate member 608 traverses permeate member 608 for most of the length of permeate member 608—except for the portion of permeate member 608 that comprises permeate reservoirs 652 and retentate reservoirs 654—and for most of the width of permeate member 608. As used herein with respect to the distribution channels in the retentate member or permeate member, “most of the length” means about 95% of the length of the retentate member or permeate member, or about 90%, 85%, 80%, 75%, or 70% of the length of the retentate member or permeate member. As used herein with respect to the distribution channels in the retentate member or permeate member, “most of the width” means about 95% of the width of the retentate member or permeate member, or about 90%, 85%, 80%, 75%, or 70% of the width of the retentate member or permeate member.

In this embodiment of a SWIIN module, the perforated member includes through-holes to accommodate ultrasonic tabs disposed on the permeate member. Thus, in this embodiment the perforated member is fabricated from 316 stainless steel, and the perforations form the walls of microwells while a membrane is used to form the bottom of the microwells. Typically, the perforations (microwells) are approximately 150 μm-200 μm in diameter, and the perforated member is approximately 125 μm deep, resulting in microwells having a volume of approximately 2.5 nL, with a total of approximately 200,000 microwells, although volumes as small as 0.1 nL may be used. The distance between the microwells is approximately 279 μm center-to-center. Though here the microwells have a volume of approximately 2.5 nl, depending on the mammalian cell type being edited the volume of the microwells may be from 5 to 100 nl, or preferably from 10 to 50 nl, and even more preferably from 10 to 25 nl. As for the membrane, membranes appropriate for use are solvent resistant, contamination free, and are able to retain the types and sizes of cells of interest. For example, in order to retain mammalian cells, the pore sizes can be as high as 10.0 μm-20.0 μm or more. Indeed, the pore sizes useful in the cell concentration device/module include filters with sizes from 0.10 μm, 0.11 μm, 0.12 μm, 0.13 μm, 0.14 μm, 0.15 μm, 0.16 μm, 0.17 μm, 0.18 μm, 0.19 μm, 0.20 μm, 0.21 μm, 0.22 μm, 0.23 μm, 0.24 μm, 0.25 μm, 0.26 μm, 0.27 μm, 0.28 μm, 0.29 μm, 0.30 μm, 0.31 μm, 0.32 μm, 0.33 μm, 0.34 μm, 0.35 μm, 0.36 μm, 0.37 μm, 0.38 μm, 0.39 μm, 0.40 μm, 0.41 μm, 0.42 μm, 0.43 μm, 0.44 μm, 0.45 μm, 0.46 μm, 0.47 μm, 0.48 μm, 0.49 μm, 0.50 μm and larger. The filters may be fabricated from any suitable material including cellulose mixed ester (cellulose nitrate and acetate) (CME), polycarbonate (PC), polyvinylidene fluoride (PVDF), polyethersulfone (PES), polytetrafluoroethylene (PTFE), nylon, or glass fiber.

The cross-section configuration of the mated serpentine channel may be round, elliptical, oval, square, rectangular, trapezoidal, or irregular. If square, rectangular, or another shape with generally straight sides, the cross section may be from about 2 mm to 15 mm wide, or from 3 mm to 12 mm wide, or from 5 mm to 10 mm wide. If the cross section of the mated serpentine channel is generally round, oval or elliptical, the radius of the channel may be from about 3 mm to 20 mm in hydraulic radius, or from 5 mm to 15 mm in hydraulic radius, or from 8 mm to 12 mm in hydraulic radius.

Serpentine channels 660 a and 660 b can have approximately the same volume or a different volume. For example, each “side” or portion 660 a, 660 b of the serpentine channel may have a volume of, e.g., 2 mL, or serpentine channel 660 a of permeate member 608 may have a volume of 2 mL, and the serpentine channel 660 b of retentate member 604 may have a volume of, e.g., 3 mL. The volume of fluid in the serpentine channel may range from about 2 mL to about 80 mL, or about 4 mL to 60 mL, or from 5 mL to 40 mL, or from 6 mL to 20 mL (note these volumes apply to a SWIIN module comprising a, e.g., 50-500K perforation member). The volume of the reservoirs may range from 5 mL to 50 mL, or from 7 mL to 40 mL, or from 8 mL to 30 mL or from 10 mL to 20 mL, and the volumes of all reservoirs may be the same or the volumes of the reservoirs may differ (e.g., the volume of the permeate reservoirs is greater than that of the retentate reservoirs).

The serpentine channel portions 660 a and 660 b of the permeate member 608 and retentate member 604, respectively, are approximately 200 mm long, 130 mm wide, and 4 mm thick, though in other embodiments, the retentate and permeate members can be from 75 mm to 400 mm in length, or from 100 mm to 300 mm in length, or from 150 mm to 250 mm in length; from 50 mm to 250 mm in width, or from 75 mm to 200 mm in width, or from 100 mm to 150 mm in width; and from 2 mm to 15 mm in thickness, or from 4 mm to 10 mm in thickness, or from 5 mm to 8 mm in thickness. In some embodiments the retentate (and permeate) members may be fabricated from PMMA (poly(methyl methacrylate)) or other materials may be used, including polycarbonate, cyclic olefin co-polymer (COC), glass, polyvinyl chloride, polyethylene, polyetheretherketone (PEEK), poly(dimethylsiloxane), polypropylene, polysulfone, polyurethane, and co-polymers of these and other polymers. Preferably at least the retentate member is fabricated from a transparent material so that the cells can be visualized. For example, a video camera may be used to monitor cell growth by, e.g., density change measurements based on an image of an empty well, with phase contrast, or if, e.g., a chromogenic marker, such as a chromogenic protein, is used to add a distinguishable color to the cells. Chromogenic markers such as blitzen blue, dreidel teal, virginia violet, vixen purple, prancer purple, tinsel purple, maccabee purple, donner magenta, cupid pink, seraphina pink, scrooge orange, and leor orange (the Chromogenic Protein Paintbox, all available from ATUM (Newark, Calif.)) obviate the need to use fluorescence, although fluorescent cell markers, fluorescent proteins, and chemiluminescent cell markers may also be used.

Because the retentate member preferably is transparent, colony growth in the SWIIN module can be monitored by automated devices such as the growth monitor sold by IncuCyte (Ann Arbor, Mich.) (see also, Choudhry, PLos One, 11(2):e0148469 (2016)).

Due to the heating and cooling of the SWIIN module, condensation may accumulate on the retentate member which may interfere with accurate visualization of the growing cell colonies. Condensation of the SWIIN module 650 may be controlled by, e.g., moving heated air over the top of (e.g., retentate member) of the SWIIN module 650, or by applying a transparent heated lid over at least the serpentine channel portion 660 b of the retentate member 604 (not shown).

In SWIIN module 650 cells and medium are flowed into serpentine channel 560 b from ports in retentate member 604, and the cells settle in the microwells while the medium passes through the membrane into serpentine channel 660 a in permeate member 608. The cells are retained in the microwells of perforated member 601 as the cells cannot travel through membrane 603. Appropriate medium may be introduced into permeate member 608 through permeate ports 611. The medium flows upward through membrane 603 to nourish the cells in the microwells (perforations) of perforated member 601. Additionally, buffer exchange can be effected by cycling medium through the retentate and permeate members.

Once editing has taken place, the cells may be flushed from the microwells by applying fluid or air pressure (or both) to the permeate member serpentine channel 660 a and thus to filter 603 and pooled. Alternatively, the cell growth medium may be removed and trypsin, collagen or pronase applied until the cells are dislodged.

FIG. 6B is a top perspective view of a SWIIN module with the retentate and perforated members in partial cross section. In this FIG. 6B, it can be seen that serpentine channel 660 a is disposed on the top of permeate member 608, is defined by raised portions 676 and traverses permeate member 608 for most of the length and width of permeate member 608 except for the portion of permeate member 608 that comprises the permeate and retentate reservoirs (note only one retentate reservoir 652 can be seen in this FIG. 6B). Moving from left to right, reservoir gasket 658 is disposed upon the integrated reservoir cover 678 (cover not seen in this FIG. 6B) of retentate member 604. Gasket 658 comprises reservoir access apertures 632 a, 632 b, 632 c, and 632 d, as well as pneumatic ports 633 a, 633 b, 633 c and 633 d. Also, at the far-left end is support 670. Disposed under permeate reservoir 652 can be seen one of two reservoir seals 662. In addition to the retentate member being in cross section, the perforated member 601 and filter 603 (filter 603 is not seen in this FIG. 6B) are in cross section. Note that there are a number of ultrasonic tabs 664 disposed at the right end of SWIIN module 650 and on raised portion 676 which defines the channel turns of serpentine channel 660 a, including ultrasonic tabs 664 extending through through-holes 666 of perforated member 601. There is also a support 670 at the end distal reservoirs 652, 654 of permeate member 608.

FIG. 6C is a side perspective view of an assembled SWIIIN module 650, including, from right to left, reservoir gasket 658 disposed upon integrated reservoir cover 678 (not seen) of retentate member 604. Gasket 658 may be fabricated from rubber, silicone, nitrile rubber, polytetrafluoroethylene, a plastic polymer such as polychlorotrifluoroethylene, or other flexible, compressible material. Gasket 658 comprises reservoir access apertures 632 a, 632 b, 632 c, and 632 d, as well as pneumatic ports 633 a, 633 b, 633 c and 633 d. Also at the far-left end is support 670 of permeate member 608. In addition, permeate reservoir 652 can be seen, as well as one reservoir seal 662. At the far-right end is a second support 670.

Imaging of cell colonies growing in the wells of the SWIIN is desired in most implementations for, e.g., monitoring both cell growth and device performance and imaging is necessary for cherry-picking implementations. Real-time monitoring of cell growth in the SWIIN requires backlighting, retentate plate (top plate) condensation management and a system-level approach to temperature control, air flow, and thermal management. In some implementations, imaging employs a camera or CCD device with sufficient resolution to be able to image individual wells. For example, in some configurations a camera with a 9-pixel pitch is used (that is, there are 9 pixels center-to-center for each well). Processing the images may, in some implementations, utilize reading the images in grayscale, rating each pixel from low to high, where wells with no cells will be brightest (due to full or nearly-full light transmission from the backlight) and wells with cells will be dim (due to cells blocking light transmission from the backlight). After processing the images, thresholding is performed to determine which pixels will be called “bright” or “dim”, spot finding is performed to find bright pixels and arrange them into blocks, and then the spots are arranged on a hexagonal grid of pixels that correspond to the spots. Once arranged, the measure of intensity of each well is extracted, by, e.g., looking at one or more pixels in the middle of the spot, looking at several to many pixels at random or pre-set positions, or averaging X number of pixels in the spot. In addition, background intensity may be subtracted. Thresholding is again used to call each well positive (e.g., containing cells) or negative (e.g., no cells in the well). The imaging information may be used in several ways, including taking images at time points for monitoring cell growth and to assure proper fluid flow in the serpentine channel 660.

FIG. 6D depicts a side view of the embodiment of the SWIIN module in FIGS. 6A-6C further comprising a heat management system including a heater and a heated cover. The heater cover facilitates the condensation management that is required for imaging. Assembly 698 comprises a SWIIN module 650 seen lengthwise in cross section, where one permeate reservoir 652 is seen. Disposed immediately upon SWIIN module 650 is cover 694 and disposed immediately below SWIIN module 650 is backlight 680, which allows for imaging. Beneath and adjacent to the backlight and SWIIN module is insulation 682, which is disposed over a heatsink 684. In this FIG. 6D, the fins of the heatsink would be in-out of the page. In addition, there is also axial fan 686 and heat sink 688, as well as two thermoelectric coolers 692, and a controller 690 to control the pneumatics, thermoelectric coolers, fan, solenoid valves, etc. The arrows denote cool air coming into the unit and hot air being removed from the unit. It should be noted that control of heating allows for growth of many different types of cells as well as cells that are, e.g., temperature sensitive, etc. Temperature control allows for protocols to be adjusted to account for differences in transformation efficiency, cell growth and viability. For more details regarding solid wall isolation incubation and normalization devices see U.S. Pat. No. 10,533,152; 10,550,363; 10,633,626; 10,633,627; 10,647,958; 10,760,043; 10,723,995; 10,844,344, 10,801,008; and 10,851,339. For alternative isolation, incubation and normalization modules, see U.S. Pat. Nos. 10,532,324; 10,625,212, 10,744,462; 10,752,874; and 10,835,869.

In addition, the SWIIN described may be adapted to dissociate cells in a manner similar to that of the TFF. That is, the SWIIN may be modified such that the retentate reservoirs, in addition to being connected through the flow channel that courses through the SWIIN device, are connected directly by a conduit where the cells are passed from one retentate reservoir to another without being sent through the flow channel. See, e.g., FIGS. 4F and 4G.

EXAMPLES

The following examples are put forth so as to provide those of ordinary skill in the art with a complete disclosure and description of how to make and use the present invention, and are not intended to limit the scope of what the inventors regard as their invention, nor are they intended to represent or imply that the experiments below are all of or the only experiments performed. It will be appreciated by persons skilled in the art that numerous variations and/or modifications may be made to the invention as shown in the specific aspects without departing from the spirit or scope of the invention as broadly described. The present aspects are, therefore, to be considered in all respects as illustrative and not restrictive.

Example I: Efficiency of Transfection, Bulk Vs. Droplets

To test the efficiency of transformation of mammalian cells in droplets, HEK293T cells were transfected with a plasmid driving expression of a fluorescent reporter molecule (dsRed). For the transfection, lipoplex solutions were prepared:

uL 20 rxns Tube 1: Optimem 25 500 L3000 1.5 30 Tube 2: Optimem 25 500 DNA (980 ng/uL) 1.02 20.4 P3000 2 40

To assemble the lipoplexes, 400 μL from each tube was loaded into separate syringes and were mixed and emulsified in a CHIPSHOP™ microfluidic droplet generator chip 162 (Jeno, Germany). The flow rates were as follows: aqueous, 500 μL per hour; hydrofluoroether (e.g., carrier phase)+fluoro-surfactant, 1 mL per hour. The droplets were incubated for 10 minutes and then demulsified with 20% perfluorooctanol in hydrofluoroether.

For the bulk transfection, 100 μL of the lipoplex solutions from each tube were mixed and 50 μL of drop-assembled or bulk-assembled lipoplex mixture to each well of previously seeded 100 K HEK293T cells in 0.5 mL complete medium.

For the in-droplet transfection, 500 μL of drop-assembled lipoplex mixture was loaded in one syringe and 500 μL of the cell suspension (at a concentration of 4M cells/mL) was loaded into a second syringe. The two mixtures were emulsified and loaded separately onto a CHIPSHOP™ microfluidic droplet generator chip 163 (Jeno, Germany) and incubated at 37° C. for 30 minutes. The flow rates were as follows: aqueous phases (lipoplex and cells), 1 mL per hour; hydrofluoroether (e.g., carrier phase)+fluoro-surfactant, 2 mL per hour. The aqueous phases were demulsified with 20% perfluorooctanol in hydrofluoroether and the sample was diluted 1:10 in complete medium. The sample was then split into two tubes with one sample being washed in complete medium. The samples were then plated. FIG. 7A depicts the lipoplex assembly and transfection processes.

Forty-eight hours after plating, cells were subjected to fluorescence-based sorting using a FACSMelody™ Cell Sorter (Becton Dickenson, Franklin Lakes, N.J.) based on dsRed reporter expression levels. The results are shown in FIG. 7B. Cells transfected with either the bulk method or the droplet method were transfected with similar efficiency (>60%) as reported by percent dsRed-positive cells.

Example II: Demonstration of Droplet Partitioning

An experiment was performed to test the integrity of cells in droplet partitions. HEK293T cells were transfected in droplets as described in Example II above in two separate transformations: one transformation was with a plasmid (EEV-CAG-BFP) driving expression of blue fluorescent protein and one transformation was with a plasmid (EEV-CAG-dsRed) driving expression of red fluorescent protein. The cells were then demulsified and pooled as shown in FIG. 8A. After pooling, the cells were split into two aliquots, with one aliquot washed one time and the other aliquot washed three times. The cells were analyzed by flow cytometry for expression of the fluorescent reporter proteins and the results are shown in FIG. 8B. Note that there was very little cross contamination between BFP+ and dsRed+ cells; that is, there was a low percentage (<3%) of BFP+ and dsRed+ cells.

FIG. 9A is a graph plotting the predicted yield of differently-sized amplified nucleic acids (e.g., 500 bp, 2000 bp and 10,000 bp) per droplet in differently-sized droplets. FIG. 9B is a graph plotting the cell coverage at 3e6 copies/cell for 500 bp amplicons for droplets of differing size.

Example III: GFP to BFP Conversion Assay

A GFP to BFP reporter cell line was created using mammalian cells with a stably integrated genomic copy of the GFP gene (HEK293T-GFP). These cell lines enabled phenotypic detection of genomic edits by various different mechanisms, including flow cytometry, fluorescent cell imaging, and genotypic detection by sequencing of the genome-integrated GFP gene. Lack of editing or perfect repair of cut events in the GFP gene result in cells that remain GFP-positive. Cut events that are repaired by the Non-Homologous End-Joining (NHEJ) pathway often result in nucleotide insertion or deletion events (indels), resulting in frame-shift mutations in the coding sequence that cause loss of GFP gene expression and fluorescence. Cut events that are repaired by the Homology-Directed Repair (HDR) pathway, using the GFP to BFP HDR donor as a repair template, result in conversion of the cell fluorescence profile from that of GFP to that of BFP.

FIG. 10 is a simplified depiction of an engine vector (described below) and amplified editing cassettes. The editing cassettes were designed that are complementary to regions proximal to the EGFP-to-BFP editing site. FIG. 11 shows an exemplary scheme for amplifying the editing cassettes in droplets. This scheme allows for the addition of a promoter, in this case the U6 promoter, to the editing cassette to produce an expression-ready cfgRNA construct. The cfgRNA cassettes comprised, from 5′ to 3′, a first priming site (P1), a gRNA spacer region (SR), a gRNA scaffold region, a donor DNA or homology arm (HA) comprising both a silent PAM mutation (SPM) and a target site mutation (TSM), and a second priming site (P2). A first primer construct comprising the U6 promoter with a region complementary to the first priming site (P1) and a second primer complementary to the second priming site were used to amplify the cfgRNA cassette, resulting in an expression cassette comprising from 5′ to 3′, the U6 promoter, the first priming site (P1), the gRNA spacer region (SR), the gRNA scaffold region, the donor DNA or homology arm (HA) comprising both the silent PAM mutation (SPM) and the target site mutation (TSM), and the second priming site (P2). In addition to the U6 promoter, the U6 primer may comprise other functional or non-functional groups (here, denoted by “R”) such as a phosphate group, an amine group, a biotin tag, a barcode and/or an NLS peptide.

Example IV: Biocompatibility of Bioreactor Materials

Biocompatibility of bioreactor relevant materials were screened in plate cultures using conditioned media. mTeSR™Plus serum-free, feeder-free cell culture medium (STEMCELL Technologies Canada INC., Vancouver, BC) was incubated with the material of interest (i.e., stainless steel and polycarbonate) for at least 72 hours at 4° C. for conditioning the cell culture media. WTC11 iPSCs were seeded on 6-well plates and conditioned media was used to grow cells in standard incubators at 37° C., 5% CO₂ and >95% relative humidity. Control cultures were grown similarly to the tested conditions except the medium was not conditioned with any materials and the medium was kept at 4° C. for 72 hours before the start of cultures.

Cells were seeded on Matrigel coated 6-well plates (CORNING® BIOCOAT™ MATRIGEL® 6-well plates (Corning, Inc., Glendale, Ariz.)) and cultured with their respective conditioned (tested sample) or unconditioned media (control) and CloneR™ (STEMCELL Technologies Canada INC., Vancouver, BC) for the first 24 hours. After the first 24 hours, cell media was exchanged with fresh conditioned (tested sample) or unconditioned media (control) without CloneR, and maintained up to 72 hours where cells reached confluency. Cell counts and viabilities were assessed at 12-hours, 36-hour and 60-hour time points after lifting cells from the Matrigel CORNING® BIOCOAT™ MATRIGEL® 6-well plates (Corning, Inc., Glendale, Ariz.) plates using RelesR™ reagent (following the manufacturer's instructions) (STEMCELL Technologies Canada INC., Vancouver, BC) and the cells were quantified on a NucleoCounter NC-200 (Chemometec, Allerod, Denmark) automated cell counting instrument following the manufacturer's instructions.

FIGS. 12A and 12B show the results of these experiments. FIGS. 12A and 12B demonstrate neither growth nor viability is impacted by the choice of materials for fabrication of the main body 504 of vessel 501 (polycarbonate), vessel lid assembly 502 (stainless steel), impeller 506 (stainless steel or polycarbonate), or medium exchange frit (stainless steel). All components were sterilized before conditioning.

Example V: Optimal Working Volume

The bioreactor described herein was tested for optimal working volume. For sensor operation, minimum optimal volume was set to 100 ml with sensor clearance at 10 mm from the bottom of the main body of the vessel. 10 million WTC11 iPSCs were seeded on 0.5 g of 10m/ml laminin L-521 coated Enhanced Attachment microcarriers (Corning, Inc., Glendale, Ariz.) in 40 ml and 100 ml mTeSR™Plus serum-free, feeder-free cell culture medium (STEMCELL Technologies Canada INC., Vancouver, BC) and CloneR (STEMCELL Technologies Canada INC., Vancouver, BC in CORNING® spinner flasks (Corning, Inc., Glendale, Ariz.). Impeller agitation was set to 70 rpm using a CHIMAREC™ direct stirrer (ThermoFisher Scientific, Waltham Mass.). A first media exchange was performed at 24 hours, and then at every 48th hour with fresh mTeSR™Plus serum-free, feeder-free cell culture medium (STEMCELL Technologies Canada INC., Vancouver, BC) (no CloneR). The cells attached to the microcarriers were quantified at 12-hour and 36-hour time points on a NucleoCounter NC-200 (Chemometec, Allerod, Denmark) automated cell counting instrument following the manufacturer's instructions. Cell counts indicated similar cell seeding efficiencies at 40 ml and 100 ml seeding volumes (data not shown).

Example VI: Assessing Growth in Bioreactor to Traditional Plating and Spinner Flask Culture

Experiments were performed to assess whether cell growth in the INSCRIPTA™ bioreactor described herein is equivalent to traditional plate and spinner flask culture conditions. Ten million WTC11 iPSCs were seeded on 0.5 g of 10 μg/ml laminin L-521 coated Enhanced Attachment microcarriers (Corning, Inc., Glendale, Ariz.) in 100 ml mTeSR™Plus serum-free, feeder-free cell culture medium (STEMCELL Technologies Canada INC., Vancouver, BC) and CloneR (STEMCELL Technologies Canada INC., Vancouver, BC) in the INSCRIPTA™ bioreactor and in CORNING® spinner flasks (Corning, Inc., Glendale, Ariz.). Impeller agitation was performed at 70 rpm for both the INSCRIPTA™ bioreactor and CORNING® spinners. A control culture was also seeded on Matrigel coated 6-well plates (CORNING® BIOCOAT™ MATRIGEL® 6-well plates (Corning, Inc., Glendale, Ariz.)) using 500 k cells per one well. The cells were maintained at 37° C., 5% CO₂ and >95% relative humidity throughout the culture period. The first media exchange was performed at 24 hours, and then at every 48th hour with fresh mTeSR™Plus serum-free, feeder-free cell culture medium (STEMCELL Technologies Canada INC., Vancouver, BC) (no CloneR) using 100 ml for microcarrier cultures and 2 ml per well for 6-well plates. Cell counts were quantified at 12-hour, 36-hour and 60-hour time points on a NucleoCounter NC-200 (Chemometec, Allerod, Denmark) automated cell counting instrument following the manufacturer's instructions.

The results are shown in FIG. 13. The graph at top shows similar numbers of iPSC cells at 10, 20, 30, 40, 50, 60, and 70 hours after seeding. The graph at bottom left shows similar results were obtained for iPSC cell expansion in three different INSCRIPTA™ bioreactors. The graph at bottom right shows the results obtained for iPSC cell expansion in four different CORNING® spinner flasks. Growth curves plotted using these cell counts indicated similar cell growth curves under the conditions tested. The 6-well plate control counts were scaled assuming an initial cell seeding number of 10 million cells for comparison. Additional INSCRIPTA™ bioreactors and CORNING® spinner flasks were seeded on different days using the same methods to compare cell growth curve variations and showed similar variation across INSCRIPTA™ bioreactors and CORNING® spinners.

Example VII: Effect of Medium Exchange

Ten million WTC11 iPSCs were seeded on 0.5 g of 10 μg/ml laminin L-521 coated Enhanced Attachment microcarriers (Corning, Inc., Glendale, Ariz.) in 100 ml mTeSR™Plus serum-free, feeder-free cell culture medium (STEMCELL Technologies Canada INC., Vancouver, BC) and CloneR (STEMCELL Technologies Canada INC., Vancouver, BC) in INSCRIPTA™ bioreactors and CORNING® spinner flasks. Impeller agitation was performed at 70 rpm for both the INSCRIPTA™ bioreactors and the CORNING® spinners. A 6-well plate control culture was also seeded on CORNING® BIOCOAT™ MATRIGEL® 6-well plates (Corning, Inc., Glendale, Ariz.) was also seeded using 500 k cells per one well. The cells were maintained at 37° C., 5% CO₂ and >95% relative humidity throughout the culture period. A first media exchange was performed at 24 hours, and then at every 48th hour with fresh mTeSR™Plus serum-free, feeder-free cell culture medium (STEMCELL Technologies Canada INC., Vancouver, BC) (no CloneR) using 100 ml for microcarrier cultures and 2 ml per well for 6-well plates. Media exchanges on the INSCRIPTA™ bioreactors were performed using a frit system as follows: Impeller agitation was stopped and the microcarriers were allowed to settle gravitationally for 5 minutes. After settling, >90% of the spent media was aspirated from the INSCRIPTA™ bioreactor through a frit connected to a peristaltic pump operating at 200 ml/min flow rate. The frit consisted of ˜100 micron pores while the microcarriers ranged from 120-225 micron in diameter. As such, microcarriers were retained in the bioreactor but spent media and dead cells were aspirated out of the bioreactor vessel. As a comparison, media exchange in CORNING® spinner flasks and 6-well plates were performed using a serological pipette connected to an aspirator (BVC Professional Aspiration System (Vacuubrand, Essex Conn.)). In all conditions, fresh media was added manually using a serological pipette. Cell counts were quantified at 20-hour, 44-hour and 68-hour time points on a NucleoCounter NC-200 (Chemometec, Allerod, Denmark) automated cell counting instrument following the manufacturer's instructions. The results of four replicates in the INSCRIPTA™ bioreactors are shown in FIG. 14. Growth curves plotted using these cell counts indicated that the media exchange approach through a frit does not have any noticeable impact on cell growth. The 6-well plate control counts were scaled assuming an initial cell seeding number of 10 million cells for comparison. During the process there was no accumulation of microcarriers on the frit in the liquid-out port.

Example VIII: Effect of Impeller Shear on Cell Viability and Reproducibility

Cell detachment from microcarriers may be achieved using an impeller agitation-based approach as follows: 10M cells were seeded on 0.5 g of 10 μg/ml laminin L-521 coated microcarriers (Corning, Inc., Glendale, Ariz.), and expanded in the INSCRIPTA™ bioreactor at 100 ml mTeSR™Plus serum-free, feeder-free cell culture medium (STEMCELL Technologies Canada INC., Vancouver, BC) at 37° C., 5% CO₂, and >95% relative humidity as described above. Once the cells reached >50 million cells as determined by cell counting, the microcarriers were allowed to settle gravitationally for 5 minutes, and >90% of the spent media was aspirated. 100 ml phosphate buffered saline (PBS) was added to microcarriers for washing and aspirated after 5 minutes. 100 ml RelesR (STEMCELL Technologies Canada INC., Vancouver, BC) was added to the microcarriers and incubated at 37° C. for 6 minutes. After 6 minutes, >90% of the RelesR (STEMCELL Technologies Canada INC., Vancouver, BC) was aspirated and 100 ml of cell media was added to the microcarriers to quench any RelesR.

At this stage, impeller agitation was performed by rotating the impeller at 2700 rpm in the clockwise direction for 15 seconds first, and then at 2700 rpm in the counter-clockwise direction for 15 seconds. This bi-directional agitation for a total of 30 seconds duration was defined as “one round” or “one cycle”. Up to five rounds/cycles of impeller agitation was tested in terms of cell detachment efficiency. After detachment, the cell and microcarrier suspension was transferred to a conical vessel. Cells and microcarriers were separated using gravitational settling where the microcarriers settle faster than the cells due to their larger diameter. In another approach, the cell and microcarrier suspension was passed through a strainer with 100 micron mesh size (e.g., CORNING® Sterile Cell strainer-100 micron, Corning, Inc., Glendale, Ariz.) to separate the cells from the microcarriers. As control, a 1 ml aliquot of microcarrier culture was detached using a P1000 pipette (PIPETMAN®) by passing the microcarriers through the pipette 5 times. After detachment, post detachment viability and the number of detached cells were quantified for assessing detachment efficiency.

The results are shown in FIG. 15. The graph at top left of FIG. 15 shows the percent post-detachment of the cells. The graph top right in FIG. 15 shows the number of viable cells/ml (×10⁵) out of ˜0.6M attached cells. The graph at bottom left in FIG. 15 shows the number of cells/ml attached out of ˜500K seeded. Finally, the graph at bottom right in FIG. 15 shows the attached fraction of cells after each cycle. Note that viability remained around 90% after all of the first, third and fifth cycles. The cells were effectively detached from the microcarriers using the impeller agitation approach and showed >90% post-detachment viability after up to 5 rounds of impeller agitation, which was similar to the control. The re-seeding efficiency of cells detached with impeller agitation were also similar to the control case where ≥70% of the detached cells were able to re-seed.

Reproducibility of impeller agitation-based passaging was tested. Ten million cells were seeded on 0.5 g of 10m/ml laminin L-521 coated microcarriers (Corning, Inc., Glendale, Ariz.), and expanded in the INSCRIPTA™ bioreactor in 100 ml mTeSR™Plus serum-free, feeder-free cell culture medium (STEMCELL Technologies Canada INC., Vancouver, BC) at 37° C., 5% CO₂, and >95% relative humidity as described above. Once the cells reached >50 million cells as determined by cell counting, the microcarriers were allowed to settle gravitationally for 5 minutes and >90% spent media was aspirated. 100 ml phosphate buffered saline (PBS) was added to the microcarriers for washing and was aspirated after 5 minutes. 100 ml RelesR (STEMCELL Technologies Canada INC., Vancouver, BC) were added to the microcarriers and incubated at 37° C. for 6 minutes. After 6 minutes, >90% of the RelesR was aspirated and 100 ml of cell media was added to the microcarriers to quench any RelesR. At this stage impeller agitation was performed by rotating the impeller at 2700 rpm in clockwise direction for 15 seconds first, and then at 2700 rpm in counter-clockwise direction for 15 seconds. This bi-directional agitation for a total of 30 seconds duration was defined as “one round” or “one cycle”. Three rounds/cycles of impeller agitation were used to detach the cells from microcarriers. After detachment, the cell and microcarrier suspension was transferred to a conical vessel. The cells and the microcarriers were separated using gravitational settling where the microcarriers settle faster than cells due to their larger diameter. Detached cells were re-seeded on fresh microcarriers at 10 million cells per 0.5 g of CORNING® laminin coated microcarriers (Corning, Inc., Glendale, Ariz.), and re-seeding efficiencies were determined based on cell counts at 24 hours after seeding. Passaging and re-seeding efficiencies are quantified and shown in the FIG. 16. FIG. 16 at top shows a simplified workflow for this process, as well as at middle a table showing the efficiency of each step, and at bottom a bar graph of passaging statistics for the indicated steps. The results indicate that impeller-based passaging is reproducible and allows for re-seeding of 30-65% of cells that were on the microcarriers prior to detachment.

Example IX: Cell Re-Seeding and Expansion after Impeller Passaging

Cell seeding and expansion after impeller passaging was tested. Ten million WTC11 cells were seeded on 0.5 g of 10 μg/ml laminin L-521 coated microcarriers (Corning, Inc., Glendale, Ariz.), and expanded in the INSCRIPTA™ bioreactor in 100 ml mTeSR™Plus serum-free, feeder-free cell culture medium (STEMCELL Technologies Canada INC., Vancouver, BC) at 37° C., 5% CO₂, and >95% relative humidity as described above. Once the cells reached >50 million cells as determined by cell counting, the impeller passaging protocol was implemented as described above. After detachment, 10M detached cells were re-seeded on 0.5 g of fresh laminin coated microcarriers (Corning, Inc., Glendale, Ariz.) and expanded as described above. As a control, an INSCRIPTA™ bioreactor was seeded with cells detached from T75 flasks detached using standard protocols. Cell counts were quantified at 20-hour, 44-hour and 68-hour time points on a NucleoCounter NC-200 (Chemometec, Allerod, Denmark) automated cell counting instrument following the manufacturer's instructions. The results are shown in FIG. 17. FIG. 17 is a graph of triplicate results demonstrating that cell seeding and expansion are unaffected by impeller-shear passaging.

Example X: Ability of Cells to Maintain Stemness

The ability of the iPSCs to retain stemness during culture and passaging was tested. Ten million cells were seeded on 0.5 g of 10 μg/ml laminin L-521 coated microcarriers (Corning, Inc., Glendale, Ariz.), and expanded in an INSCRIPTA™ bioreactor in mTeSR™Plus serum-free, feeder-free cell culture medium (STEMCELL Technologies Canada INC., Vancouver, BC) at 37° C., 5% CO₂, and >95% relative humidity as described above. Once the cells reached >50 million cells as determined by cell counting, the impeller passaging protocol was implemented and 10M detached cells were re-seeded onto fresh 0.5 g laminin coated microcarriers (Corning, Inc., Glendale, Ariz.). This process was repeated two more times and the cells were stained after final detachment using antibodies (BIOLEGEND®, San Diego Calif.) specific to three stemness expression markers (TRA-1-60, OCT-3/4 and SOX-2) following the manufacturer's instructions, followed by analysis using flow cytometry (BD FACSMelody™) (Becton Dickinson, Inc., Franklin Lakes, N.J.). Cells grown and impeller passaged on the INSCRIPTA™ bioreactors showed expression of stemness markers similar to the cells grown on Matrigel (CORNING® BIOCOAT™ MATRIGEL® 6-well plates (Corning, Inc., Glendale, Ariz.)) and laminin coated plates (CORNING® BIOCOAT™ laminin plates (Corning, Inc., Glendale, Ariz.)).

Stemness antibody staining was performed in the following manner, with the equipment and materials listed in Table 1:

TABLE 1 Foxp3/Transcription Factor Fixation/Permeabilization Concentrate and Diluent, ThermoFisher Scientific, cat. # 00-5521-00 eBioscience ™ Flow Cytometry Staining Buffer, ThermoFisher Scientific, cat. # 00-4222-26 Anti-SOX2 (Brilliant Violet 421): Biolegend, cat. # 656114 Anti-OCT3/4 (Alexa488): Biolegend, cat. # 653706 Anti-TRA-1-60 (PE-Cy7): Biolegend, cat. # 330620 Anti-CD44 (PE-Cy5): ThermoFisher Scientific, cat. # 15-0441-82 Anti-CD13 (PE-Cy7): Biolegend, cat. # 301712 Anti-NESTIN (Alexa488): Biolegend, cat. # 656812 Anti-SSEA4 (V450): BD Biosciences, cat. # 561156 FACSMelody ™ flow cytometer (Becton Dickinson, Inc., Franklin Lakes, NJ)

In a first step, a single-cell suspension was prepared and centrifuged 5 minutes at 200×g. The cells were then washed in an appropriate volume of DPBS and centrifuged again for 5 minutes at 200×g. The supernatant was discarded and the pellet was vortexed to dissociate the pellet. Fresh Foxp3 fixation/permeabilization working solution (ThermoFisher Scientific, Waltham, Mass.) was prepared by mixing one part Foxp3 fixation/permeabilization concentrate with three parts Foxp3 fixation/permeabilization diluent and 1 ml was added to each tube and each tube was then vortexed. The vortexed cells and fixation/permeabilization working solution were incubated for 30-60 minutes in the dark at room temperature. A 1× working solution of permeabilization buffer was prepared by mixing 1 part 10× permeabilization buffer with 9 parts dH₂O and 2 ml was added to each sample. The cells were centrifuged at 400-600×g for 5 minutes at room temperature and the supernatant was discarded. The cell pellet was resuspended in 1× permeabilization buffer for a total volume of approximately 100 μl. The cells were diluted so that there were no more than 10,000 cells/μl, and 1M cells were transferred to a fresh tube. The appropriate amount of directly-conjugated antibody was dispensed into each tube. The cells were incubated for >30 minutes in the dark at room temperature. Two ml of 1× permeabilization buffer was added to each tube and the samples were centrifuged at 400-600×g for 5 minutes at room temperature and the supernatant was discarded. The stained cells were suspended in flow cytometry staining buffer.

The results are shown in FIG. 18. FIG. 18 at top are histograms showing the fluorescent expression distribution measured via flow cytometry of the cell population for individual sternness marker expression. The x-axis shows the fluorescence signal and the y-axis shows cell count. BR1 indicates results for INSCRIPTA™ bioreactor 1, BR2 indicates results for INSCRIPTA™ bioreactor 2 (replicate), L1 indicates CORNING® BIOCOAT™ laminin plates (Corning, Inc., Glendale, Ariz.), L2 indicates CORNING® BIOCOAT™ laminin plates (Corning, Inc., Glendale, Ariz.) (replicate), M1 indicates CORNING® BIOCOAT™ MATRIGEL® 6-well plates (Corning, Inc., Glendale, Ariz.), and M2 indicates CORNING® BIOCOAT™ MATRIGEL® 6-well plates (Corning, Inc., Glendale, Ariz.) (replicate). A dark control was used for comparison where the cells in one well from the M1 6-well plate are prepared as the experimental cells but were not stained with antibodies. Looking at the graph at bottom left of FIG. 18, note that the percent of cells positive for the TRA-1-60 and SOX2 cell surface markers was similar across culture conditions. Cell surface marker OCT3/4 was a little lower (94-96%) in the cells grown in the INSCRIPTA™ bioreactors than in the laminin plates (98%) and in the MATRIGEL® plates (98%). The graph at right of FIG. 18 shows the median fluorescence obtained for each of TRA 1-60, OCT3/4 and SOX2 markers for each bioreactor, laminin plate and MATRIGEL® plate replicate.

Example XI: Ability of Cells to Maintain Differentiation Potential

To test whether cells grown in the INSCRIPTA™ bioreactor would retain differentiation potential, ten million cells were seeded on 0.5 g of 10 μg/ml laminin L-521 coated microcarriers (Corning, Inc., Glendale, Ariz.), and expanded in INSCRIPTA™ Bioreactor in 100 ml mTeSR™Plus serum-free, feeder-free cell culture medium (STEMCELL Technologies Canada Inc., Vancouver, BC) at 37° C., 5% CO₂, and >95% relative humidity as described above. Once the cells reached >50 million cells as determined by cell counting, the impeller passaging protocol as described above in Example VII was implemented and 10M detached cells were re-seeded onto 0.5 g fresh laminin coated microcarriers. This process was repeated two more times, and after the final detachment the cells were seeded on 12-well plates for trilineage differentiation using a commercial protocol (STEMDIFF™ Trilinage Differentiation Kit, STEMCELL Technologies Canada Inc., Vancouver, BC). After trilineage differentiation, the cells from each lineage were stained with antibodies specific to markers specific to that lineage (available from BIOLEGEND®, San Diego Calif. and Miltenyi Biotec, San Diego, Calif.) following the manufacturer's instructions. The cells grown and impeller-passaged on the INSCRIPTA™ bioreactors showed expression of lineage-specific markers similar to the cells grown on Matrigel and laminin coated plates.

The tri-lineage differentiation antibody staining protocol was performed in the following manner, with the equipment listed in Table 2 and the antibodies listed in Table 3:

TABLE 2 Foxp3/Transcription Factor Fixation/Permeabilization Concentrate and Diluent, ThermoFisher Scientific, cat. # 00-5521-00 eBioscience ™ Flow Cytometry Staining Buffer, ThermoFisher Scientific, cat. # 00-4222-26 FACS staining buffer (2% FBS, 1 mM EDTA, 0.5% BSA) FACS buffer (2% FBS, 1 mM EDTA) FACSMelody ™ flow cytometer (Becton Dickinson, Inc., Franklin Lakes, NJ)

TABLE 3 Cell Antibody Marker Type Link Catalog # Conjugate Isotype Isotype Conc. CXCR4 Mesoderm BioLegend 306518 BV421 Mouse BioLegend 1:200 IgG2a, κ NCAM1 Mesoderm BioLegend 362510 PE-Cy7 Mouse BioLegend 1:200 IgG1, κ Brachyury Mesoderm SantaCruz sc- AF488 Mouse BioLegend 1:25  374321 IgG2b, κ AF488 Nestin Ectoderm BioLegend 656808 BV421 Mouse BioLegend 1:400 IgG2a, κ Otx-2 Ectoderm Miltenyi 130-121- Vio B515 recombinant Miltenyi 1:100 202 hs IgG1 PAX6 Ectoderm Miltenyi 130-123- PE recombinant Miltenyi 1:400 250 hs IgG1 CXCR4 Endoderm BioLegend 306518 BV421 Mouse BioLegend 1:400 IgG2a, κ SOX17 Endoderm Miltenyi 130-111- Vio B515 recombinant Miltenyi 1:600 147 hs IgG1 FOXA2 Endoderm BD 561589 PE Mouse BD >1:20  Biosciences IgG1, κ Biosciences

A single-cell suspension was prepared by lifting cells with TrypLE™ SELECT (ThermoFisher Scientific, Waltham, Mass., USA) and was centrifuged for 5 minutes at 200×g. The cells were washed in DPBS and centrifuged a second time. The cells were fixed with a Foxp3 kit (ThermoFisher Scientific, Waltam, Mass.) according to the manufacturer's instructions. Following incubation at room temperature in the dark for 30-60 minutes, 1 ml Foxp3 fixation/permeabilization working solution was added. Each sample contained ≤10M cells. A 1× working solution of permeabilization buffer was prepared by mixing 1 part of 10× Permeabilization Buffer with 9 parts of distilled water and 2 ml of 1x permeabilization buffer was added to each tube. The samples were centrifuged at 400-600×g for 5 minutes at room temperature. The supernatant was discarded and the pellet was resuspended in residual volume of 1× permeabilization buffer for a total volume of approximately 100 μl. The cells were diluted so that there were no more than 10,000 cells/μl in a 96-well V- or U-bottom plate. A master mix of antibodies per cell lineage in FACS staining buffer was prepared. Approximately 500,000 cells were stained in 50 μl of staining solution. The cells were incubated on ice in the dark for at least 30 minutes. 150 μl of FACS buffer was added to each well. The cells were then centrifuged at 500×g for 5 minutes at room temperature and the supernatant was discarded. The cells were resuspended in FACS buffer and analyzed by a flow cytometer on the FACSMelody™ flow cytometer.

The results are shown in FIG. 19A-19F. FIGS. 19A, 19C and 19E comprise bar graphs showing % positive cells for endoderm markers CXCR4 and SOX17; mesoderm markers NCAM1 and CXCR4; and ectoderm markers NESTIN, OTX2 and PAX6. FIGS. 19B, 19D and 19E comprise bar graphs showing median fluorescence obtained for the endoderm, mesoderm and ectoderm markers. BR1 indicates results for INSCRIPTA™ bioreactor 1, BR2 indicates results for INSCRIPTA™ bioreactor 2 (replicate), L1 indicates CORNING® BIOCOAT™ laminin plates (Corning, Inc., Glendale, Ariz.), L2 indicates CORNING® BIOCOAT™ laminin plates (Corning, Inc., Glendale, Ariz.) (replicate), M1 indicates CORNING® BIOCOAT™ MATRIGEL® 6-well plates (Corning, Inc., Glendale, Ariz.), and M2 indicates CORNING® BIOCOAT™ MATRIGEL® 6-well plates (Corning, Inc., Glendale, Ariz.) (replicate). Note that the cells grown in the bioreactors maintain differentiation potential roughly equivalent to cells grown in the laminin plates and MATRIGEL® plates. A pluripotent control was used, where the pluripotent control were cells that were not differentiated using the STEMDIFF medium (STEMDIFF™ Trilinage Differentiation Kit, STEMCELL Technologies Canada Inc., Vancouver, BC) but were maintained in mTeSRPlus medium (STEMCELL Technologies Canada INC., Vancouver, BC).

While this invention is satisfied by embodiments in many different forms, as described in detail in connection with preferred embodiments of the invention, it is understood that the present disclosure is to be considered as exemplary of the principles of the invention and is not intended to limit the invention to the specific embodiments illustrated and described herein. Numerous variations may be made by persons skilled in the art without departure from the spirit of the invention. The scope of the invention will be measured by the appended claims and their equivalents. The abstract and the title are snot to be construed as limiting the scope of the present invention, as their purpose is to enable the appropriate authorities, as well as the general public, to quickly determine the general nature of the invention. In the claims that follow, unless the term “means” is used, none of the features or elements recited therein should be construed as means-plus-function limitations pursuant to 35 U.S.C. § 112, ¶6. 

We claim:
 1. A method of transfecting and performing nucleic acid-guided nuclease editing in mammalian cells in an automated editing instrument comprising the steps of: providing an automated closed cell editing instrument comprising a growth module and a microfluidic module; growing mammalian cells in the growth module; synthesizing a library of editing cassettes off-instrument, wherein each editing cassette comprises a different gRNA and donor DNA pair; generating, in the microfluidic module, a first plurality of aqueous droplets in a first immiscible carrier fluid, wherein the first plurality of aqueous droplets comprises dNTPs, primers, polymerase and an editing cassette, and wherein each aqueous droplet of the first plurality of aqueous droplets on average comprises one or no editing cassette; providing, in the microfluidic module, conditions to allow amplification of the editing cassettes in the first plurality of aqueous droplets; separating aqueous droplets with amplified editing cassettes from aqueous droplets without amplified editing cassettes; generating, in the microfluidic module, a second plurality of aqueous droplets in a second immiscible carrier fluid, wherein the second plurality of aqueous droplets comprises transfection reagents and a nucleic acid-guided nuclease or nuclease fusion or a coding sequence for a nucleic acid-guided nuclease or nuclease fusion; adding, in the microfluidic module, the first plurality of aqueous droplets with the amplified editing cassettes to the second immiscible carrier fluid comprising the second plurality of aqueous droplets; merging, in the microfluidic module, on average one of the first plurality of aqueous droplets with the amplified editing cassette with on average one of the second plurality of aqueous droplets comprising transfection reagents resulting in aqueous droplet reagent bundles; generating, in the microfluidic module, a third plurality of aqueous droplets in a third immiscible carrier fluid, wherein the third plurality of aqueous droplets comprises the mammalian cells grown in the growth module; adding, in the microfluidic module, the aqueous droplet reagent bundles to the third immiscible carrier fluid comprising the third plurality of aqueous droplets comprising the mammalian cells; merging, in the microfluidic module, on average one aqueous droplet reagent bundle with on average one aqueous droplet comprising the mammalian cells to produce merged droplets; providing, in the microfluidic module, conditions for cell transfection and editing; transferring the merged droplets to the growth module; and demulsifying the merged droplets in the growth module resulting in pooled merged droplets.
 2. The method of claim 1, wherein the growth module is a rotating growth module, a tangential flow filtration module or a bioreactor module.
 3. The method of claim 2, wherein the growth module is a rotating growth module.
 4. The method of claim 2, wherein the growth module is a tangential flow filtration module.
 5. The method of claim 2, wherein the growth module is a bioreactor.
 6. The method of claim 1, wherein the first, second and third immiscible carrier fluids are the same immiscible carrier fluid.
 7. The method of claim 6, wherein the first, second and third immiscible carrier fluids are fluorinated oils.
 8. The method of claim 1, wherein at least two of the first, second and third immiscible carrier fluids are different immiscible carrier fluids.
 9. The method of claim 1, wherein the mammalian cells are grown on microcarriers.
 10. The method of claim 1, wherein the merging step is accomplished by a localized electric field, providing locally a chemical that disrupts or destabilizes the surfactant in the second and/or third immiscible carrier fluids, or use of a textured surface in a flow path of a microfluidic channel through which the second and/or third immiscible carrier fluids flow.
 11. The method of claim 1, wherein the step of separating aqueous droplets with amplified editing cassettes from aqueous droplets without amplified editing cassettes is accomplished by electrophoresis; dielectricphoresis; acoutstrophoresis; optical sorting; or magnetophoresis.
 12. The method of claim 11, wherein the step of separating aqueous droplets with amplified editing cassettes from aqueous droplets without amplified editing cassettes is accomplished by optical sorting.
 13. A method of transfecting and performing nucleic acid-guided nuclease editing in mammalian cells in an automated editing instrument comprising the steps of: providing an automated closed cell editing instrument comprising a growth module, a microfluidic module and a solid wall module; growing mammalian cells in the growth module; synthesizing a library of editing cassettes off-instrument, wherein each editing cassette comprises a different gRNA and donor DNA pair; generating, in the microfluidic module, a first plurality of aqueous droplets in a first immiscible carrier fluid, wherein the first plurality of aqueous droplets comprise dNTPs, primers, polymerase, a nucleic acid-guided nuclease or nuclease fusion or a coding sequence for a nucleic acid-guided nuclease or nuclease fusion and an editing cassette, wherein each aqueous droplet of the first plurality of aqueous droplets on average comprises one or no editing cassette; polymerizing, in the microfluidic module, the first plurality of aqueous droplets resulting in reagent bundle gel beads; providing, in the microfluidic module, conditions to allow amplification of the editing cassettes in the reagent bundle gel beads; separating reagent bundle gel beads with amplified editing cassettes from reagent bundle gel beads without amplified editing cassettes; delivering the reagent bundle gel beads comprising amplified editing cassettes to a solid wall module comprising wells, wherein the wells comprise the mammalian cells and are sized so as to be able to accommodate only one reagent bundle gel bead; dissolving, in the solid wall module, the reagent bundle gel beads comprising amplified editing cassettes in the wells; providing transfection reagents to the wells in the solid wall module; providing conditions to allow transfection and editing in the mammalian cells in the solid wall module; growing the mammalian cells in the solid wall module; dislodging the mammalian cells from the wells in the solid wall module; and pooling the cells.
 14. The method of claim 13, wherein the growth module is a rotating growth module, a tangential flow filtration module or a bioreactor module.
 15. The method of claim 14, wherein the growth module is a rotating growth module.
 16. The method of claim 14, wherein the growth module is a tangential flow filtration module.
 17. The method of claim 14, wherein the growth module is a bioreactor.
 18. The method of claim 13, wherein the first, second and third immiscible carrier fluids are the same immiscible carrier fluid.
 19. The method of claim 18, wherein the first, second and third immiscible carrier fluids are fluorinated oils.
 20. The method of claim 13, wherein at least two of the first, second and third immiscible carrier fluids are different immiscible carrier fluids.
 21. The method of claim 13, wherein the mammalian cells are grown on microcarriers.
 22. The method of claim 13, wherein the step of separating aqueous droplets with amplified editing cassettes from aqueous droplets without amplified editing cassettes is accomplished by electrophoresis; dielectricphoresis; acoutstrophoresis; optical sorting; or magnetophoresis.
 23. The method of claim 22, wherein the step of separating aqueous droplets with amplified editing cassettes from aqueous droplets without amplified editing cassettes is accomplished by optical sorting.
 24. The method of claim 13, wherein the solid wall module is a solid wall isolation, incubation, and normalization (SWIIN) module.
 25. The method of claim 24, wherein the SWIIN module comprises microwells with a volume of approximately 2.5 nl.
 26. The method of claim 24, wherein the SWIIN module comprises 200,000 microwells.
 27. The method of claim 24, wherein the SWIIN module comprises a heater and a heated cover.
 28. The method of claim 13, wherein the reagent bundle gel beads comprise polyacrylamide with disulfide crosslinkers.
 29. The method of claim 28, wherein the reagent bundle gel beads are dissolved by exposure of the reagent bundle gel beads to a reducing agent.
 30. The method of claim 29, wherein the reducing agent is β-mercaptoethanol, dithiothreitol (DTT), (2S)-2-amino-1,4-dimercaptobutane (dithiobutylamine or DTBA), or tris(2-carboxyethyl) phosphine (TCEP). 